Alignments for a candidate for asnB in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Herbaspirillum seropedicae SmR1

Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate HSERO_RS13795 HSERO_RS13795 asparagine synthase

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__HerbieS:HSERO_RS13795
          Length = 647

 Score =  347 bits (889), Expect = 1e-99
 Identities = 212/635 (33%), Positives = 349/635 (54%), Gaps = 42/635 (6%)

Query: 1   MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60
           MCG  G+F+ H  A+     +L+ +MN+   HRGPD  G   +  +G G RRLSI+D+ +
Sbjct: 1   MCGITGIFSLHGQAEI--DRQLLARMNETQHHRGPDEGGLHVEAGLGLGHRRLSIVDLSS 58

Query: 61  GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120
           G QPL  ED +  ++FNG IYNY EL  EL A G+ F +  DTEV++  +  +  +  ++
Sbjct: 59  GQQPLFNEDGSVVVVFNGMIYNYRELMRELTALGHQFRSRCDTEVIVHAWEQWGRDCVTR 118

Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTIND-QVYFASERKSLMV-AQNDIEIDK 178
           LRGMFAF +W++    L+ ARD  GIKPL+Y  + D +  FASE K+L+        +D 
Sbjct: 119 LRGMFAFALWDRQRQTLFVARDRLGIKPLFYALLPDGRFLFASELKALLADPALPRALDP 178

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIR---PDGDITFKTYFKANFK-PVQTEE 234
            A+++Y ++ +VPEP T+   V K+ PG    ++     G    + Y+   F+   Q   
Sbjct: 179 CAVEEYFAYGYVPEPRTILRGVHKLSPGHTLLLQRGATRGQPQQQRYWDIPFQLGSQRPA 238

Query: 235 DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVS-VAKEFHPSLKTFSVGFEQQ 293
           +++  E+ + + + V  H+ +DV +G FLSGG+DSS +V+ +A+    S+ T S+ F   
Sbjct: 239 EEIAAELLERLREVVGSHLVTDVSLGGFLSGGVDSSAVVAMMAQLTGESVNTCSIAFNDP 298

Query: 294 GFSEVDVAKETAAALGIENISKVISPEEY--MNELPKIVWHFDDPLADPAAIPLYFVAKE 351
            + E   A + A      +  + +  ++Y  ++ L K+   +D+P AD +AIP Y V + 
Sbjct: 299 AYDESHYAAQVAQQFRTRHHMRTVDKDDYGLIDLLAKL---YDEPYADSSAIPTYRVCQL 355

Query: 352 AKKHVTVALSGEGADELFGGYNIYREPLS-LKPFERIPSGLKKMLLHV-------AAVMP 403
           AK+ VTVALSG+G DE F GY  YR  ++  K   R+P GL+K L          A   P
Sbjct: 356 AKESVTVALSGDGGDENFAGYRRYRYAMNEEKVRARLPEGLRKPLFGFLGRHYPKADWAP 415

Query: 404 EGMRGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLKHYNPNLSYR-------DVTKTYF 456
             +R K+  E       + Y     I  + V+++LL   +P L          +V + + 
Sbjct: 416 RVLRAKTTFEALARDTVEGYFHGVSIMPDRVRQRLL---SPGLRRELQGYQAIEVMRGHA 472

Query: 457 TESSSYSDINKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDEL 516
            ++ +   ++ +QY+D+ T++ GDIL K D+ +MA++LE+RVP LD    +  S +P  L
Sbjct: 473 AQAPTEDALSLLQYLDLKTYLPGDILTKVDRASMAHALEVRVPLLDHQFVEWVSGLPPAL 532

Query: 517 KTKNGTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYI 576
           K   G  KY+ +KA EG + E +L R+K+GF +P+  WL+  +    R ++Q+S     +
Sbjct: 533 KLHEGQGKYIFKKALEGTLSEDILYRRKMGFSIPLSSWLRGPL----RQVVQDSLLGPLL 588

Query: 577 HK------DYVLQLLEDHCADKADNSRKIWTVLIF 605
            +      D+V +L+E H + + D++  +W +L+F
Sbjct: 589 RQTGLFDMDFVQELVEQHQSGRRDHAAPLWALLMF 623


Lambda     K      H
   0.319    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 932
Number of extensions: 43
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 632
Length of database: 647
Length adjustment: 38
Effective length of query: 594
Effective length of database: 609
Effective search space:   361746
Effective search space used:   361746
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate HSERO_RS13795 HSERO_RS13795 (asparagine synthase)
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01536.hmm
# target sequence database:        /tmp/gapView.24999.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                  Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.3e-152  494.5   0.0   2.6e-152  494.3   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS13795  HSERO_RS13795 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS13795  HSERO_RS13795 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.3   0.0  2.6e-152  2.6e-152       1     517 []       2     563 ..       2     563 .. 0.90

  Alignments for each domain:
  == domain 1  score: 494.3 bits;  conditional E-value: 2.6e-152
                                  TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsne 68 
                                                Cgi+gi+ l+ +a+ +++ +++m+et++hRGPD+ g++ +   ++ +lghrRL+i+dls+g+QPl ne
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795   2 CGITGIFSLHGQAEIDRQLLARMNETQHHRGPDEGGLHVE---AGLGLGHRRLSIVDLSSGQQPLFNE 66 
                                                ***********999999*******************9999...8************************ PP

                                  TIGR01536  69 k.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkge 135
                                                + +vv+vfnG IYN++eL +el + G++F++++DtEVi++a+e+wg+++v rL+GmFAfalwd+++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795  67 DgSVVVVFNGMIYNYRELMRELTALGHQFRSRCDTEVIVHAWEQWGRDCVTRLRGMFAFALWDRQRQT 134
                                                ******************************************************************** PP

                                  TIGR01536 136 lflaRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevke 202
                                                lf+aRDrlGikPL+ya   +g++lfaSE+Kalla ++ +++ld  a+ e++++ +vp+++t+ ++v++
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795 135 LFVARDRLGIKPLFYALLpDGRFLFASELKALLADPALPRALDPCAVEEYFAYGYVPEPRTILRGVHK 202
                                                ****************999************************************************* PP

                                  TIGR01536 203 lepakal.......dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGG 262
                                                l+p++ l       +g+ + ++yw++  +   +   ee  +el e l++ v ++lv+dv +g +lSGG
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795 203 LSPGHTLllqrgatRGQPQQQRYWDIPFQLgSQRPAEEIAAELLERLREVVGSHLVTDVSLGGFLSGG 270
                                                *******999888777777777*******9778889999***************************** PP

                                  TIGR01536 263 lDSslvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevila 330
                                                +DSs+v+a++++   ++v+t si+f+ ++++des++a++va++++t+h+  +++++++   ++ +   
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795 271 VDSSAVVAMMAQLTGESVNTCSIAFN-DPAYDESHYAAQVAQQFRTRHHMRTVDKDDY-GLIDLLAKL 336
                                                **************************.*****************************97.467777788 PP

                                  TIGR01536 331 leeptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale.............. 384
                                                 +ep a++++ip+y +++la+e  v+V+LsG+G+DE f+GY ++r a +ee+++              
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795 337 YDEPYADSSAIPTYRVCQLAKES-VTVALSGDGGDENFAGYRRYRYAMNEEKVRarlpeglrkplfgf 403
                                                89*********************.******************************99888888888888 PP

                                  TIGR01536 385 .................lpeaselaekkl.............llqaklakeselkellkakleeelk. 421
                                                                            +             ++  +++   + ++ll+  l++el+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795 404 lgrhypkadwaprvlraK----------TtfealardtvegyFHGVSIMPDRVRQRLLSPGLRRELQg 461
                                                888877755533322220..........1344666677788855555555555555555544444441 PP

                                  TIGR01536 422 .....ekeelkkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsip 483
                                                      ++ ++++ ++e +l+ l++ldl+++l+++++ k Dr+smah lEvRvP+lD+++ve +  +p
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795 462 yqaieVMRGHAAQAPTEDALSLLQYLDLKTYLPGDILTKvDRASMAHALEVRVPLLDHQFVEWVSGLP 529
                                                0000044455555666699************************************************* PP

                                  TIGR01536 484 pelklrdgkeKvlLreaaeellPeeileRkKeaf 517
                                                p lkl++g+ K+++++a+e+ l e+il+R+K++f
  lcl|FitnessBrowser__HerbieS:HSERO_RS13795 530 PALKLHEGQGKYIFKKALEGTLSEDILYRRKMGF 563
                                                ********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (647 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 10.49
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis