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_RS21060 HSERO_RS21060 hypothetical protein

Query= CharProtDB::CH_005185
         (632 letters)



>FitnessBrowser__HerbieS:HSERO_RS21060
          Length = 581

 Score =  286 bits (731), Expect = 2e-81
 Identities = 187/583 (32%), Positives = 299/583 (51%), Gaps = 22/583 (3%)

Query: 1   MCGFVGVF-NKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVE 59
           MCG  G+  N+  L   +    +++ M   +  RGPD +G      +G   RRLSI D+ 
Sbjct: 1   MCGIAGILMNQAALPDVS----VLRAMAASMAFRGPDDEGIHVAPSIGLVHRRLSIRDLS 56

Query: 60  NGGQ-PLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAA 118
           + G  P+S  D  Y ++FNGEIYN+ ELR ELE+ G  F++ SDTEV+L  Y  +  +  
Sbjct: 57  SAGHCPMSTADGRYTLVFNGEIYNWRELRAELESMGQVFHSQSDTEVVLQAYNAWGTDVI 116

Query: 119 SKLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDK 178
           ++L GMFA  +W+     L+ ARD  G KPLYY   +  + F+S   +++ A   + +D 
Sbjct: 117 ARLEGMFALAVWDDQAGSLFLARDRMGEKPLYYARTDQGLAFSSSPSAVLHATGPLPLDP 176

Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYF---KANFKPVQTEED 235
             +  ++S  F+P   T  A ++ + P +      DG I  + Y+   + + KP+   + 
Sbjct: 177 MGIACHLSHTFIPATHTGWAGLRVLAPATWLLAHADGRIEERRYWDFPRTSPKPIAWAD- 235

Query: 236 KLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPSLKTFSVGFEQQGF 295
             + EV   + DSV   + +DV VG FLSGG+DSS I ++A   +  +K FS+GF +  +
Sbjct: 236 -ALSEVESILDDSVQRTLDADVEVGVFLSGGVDSSLIAALAARHNKRVKAFSIGFAEVQY 294

Query: 296 SEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKH 355
           +E+  ++  A  LGIE    +++ ++ ++ LP +V  +  P  D +A+P Y V++ A++H
Sbjct: 295 NELPYSEAVAKHLGIEQHVHIVTCDDIIDALPHLVRQYGQPFGDASALPTYLVSRLARQH 354

Query: 356 VTVALSGEGADELFGGY-NIYREPLSLKPFERIPSGLKKMLLHVAAVMPEGMRGKSLLER 414
             V LSG+G DELFGGY  +     + +    +P+ L++  +  A     G  G+ L   
Sbjct: 355 AKVCLSGDGGDELFGGYWRLQAGVYAARYGALVPTWLRRHAV-PAVASRLGRLGRRLDAM 413

Query: 415 GCTPLQDRYIGNAKIFEESVKKQLLKHYNPN-LSYRDVTKTY------FTESSSYSDINK 467
               L +   G+     ES    L +   PN L   D+ K         T     S + +
Sbjct: 414 NTLSLAE--AGSGYTNSESWFNHLQQVAGPNLLPALDMEKLVAARVGKATNRPEASIVQR 471

Query: 468 MQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLL 527
           + Y DI       +L K D  +MA SLE+R PFL   + + A  +PD  K K G  K LL
Sbjct: 472 LLYDDIQIQFPDALLAKVDVASMAASLEVREPFLTPRLLEFAWGLPDHTKLKWGNRKALL 531

Query: 528 RKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQES 570
           ++ A   VP  V+ R K+GF  P+  W K E+ E+  ++ + S
Sbjct: 532 KEIAARHVPRDVVYRPKMGFASPLDKWFKGELGEYGASLFEHS 574


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: 772
Number of extensions: 36
Number of successful extensions: 4
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: 581
Length adjustment: 37
Effective length of query: 595
Effective length of database: 544
Effective search space:   323680
Effective search space used:   323680
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: 53 (25.0 bits)

Align candidate HSERO_RS21060 HSERO_RS21060 (hypothetical protein)
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.24010.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.7e-131  424.6   0.0   4.2e-131  424.3   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS21060  HSERO_RS21060 hypothetical prote


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS21060  HSERO_RS21060 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.3   0.0  4.2e-131  4.2e-131       1     517 []       2     551 ..       2     551 .. 0.89

  Alignments for each domain:
  == domain 1  score: 424.3 bits;  conditional E-value: 4.2e-131
                                  TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsn 67 
                                                Cgiagi+ ++a++ +  + +++m+  +a RGPD+eg++        +l+hrRL+i dls++ + P+s 
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060   2 CGIAGILMNQAALPD-VSVLRAMAASMAFRGPDDEGIHVA---PSIGLVHRRLSIRDLSSAgHCPMST 65 
                                                *********998777.589*****************9888...79*************9998****** PP

                                  TIGR01536  68 ek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkg 134
                                                ++ ++++vfnGEIYN +eLr+ele  G  F+++sDtEV+L+ay++wg ++++rLeGmFA+a+wd+++g
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060  66 ADgRYTLVFNGEIYNWRELRAELESMGQVFHSQSDTEVVLQAYNAWGTDVIARLEGMFALAVWDDQAG 133
                                                ******************************************************************** PP

                                  TIGR01536 135 elflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevke 202
                                                 lflaRDr+G kPLYya++++ l+f+S   a+l++   +  ld  ++a  l++ + p  +t +++++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060 134 SLFLARDRMGEKPLYYARTDQGLAFSSSPSAVLHAT-GPLPLDPMGIACHLSHTFIPATHTGWAGLRV 200
                                                *******************************99998.4666777777777777777999********* PP

                                  TIGR01536 203 lepakal....dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDS 265
                                                l pa  l    dg  + ++yw+  +++ +     ++ +e+++ l d+v++ l adv+vgv+lSGG+DS
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060 201 LAPATWLlahaDGRIEERRYWDFPRTSpKPIAWADALSEVESILDDSVQRTLDADVEVGVFLSGGVDS 268
                                                *****99995555555555***9999866677899********************************* PP

                                  TIGR01536 266 slvaaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilalee 333
                                                sl+aa+a+++ k +vk Fsigf+ + +++e  + ++va++lg+e +  +++ ++++++l++++++  +
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060 269 SLIAALAARHNK-RVKAFSIGFA-EVQYNELPYSEAVAKHLGIEQHVHIVTCDDIIDALPHLVRQYGQ 334
                                                **********88.9*********.9******************************************* PP

                                  TIGR01536 334 ptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale................. 384
                                                p+ ++++ p+yl+s+lar++  kV LsG+G+DElfgGY + +    +++                   
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060 335 PFGDASALPTYLVSRLARQH-AKVCLSGDGGDELFGGYWRLQAGVYAARYGalvptwlrrhavpavas 401
                                                ********************.******************99988777777778777777666555544 PP

                                  TIGR01536 385 .......lpeaselaekkl...................llqaklakeselkellkakleeelkekeel 426
                                                                  l                      ++l++    + l   ++e+ ++ +  +
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060 402 rlgrlgrR----------LdamntlslaeagsgytnseSWFNHLQQVAGPNLLPALDMEKLVAARVGK 459
                                                44444440..........04444555556566663222222333444444556667888888888888 PP

                                  TIGR01536 427 kkelkeeseleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgke 493
                                                +++++e+s +++ll++d++   +d l+ak D +sma slEvR Pfl  +l+e+a+ +p   kl+ g++
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060 460 ATNRPEASIVQRLLYDDIQIQFPDALLAKvDVASMAASLEVREPFLTPRLLEFAWGLPDHTKLKWGNR 527
                                                8888888************************************************************* PP

                                  TIGR01536 494 KvlLreaaeellPeeileRkKeaf 517
                                                K lL+e+a++++P+++++R+K++f
  lcl|FitnessBrowser__HerbieS:HSERO_RS21060 528 KALLKEIAARHVPRDVVYRPKMGF 551
                                                **********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (581 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.98
//
[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