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 Putative asparagine synthetase [glutamine-hydrolyzing] 2; EC 6.3.5.4 (uncharacterized)
to candidate HSERO_RS21005 HSERO_RS21005 asparagine synthase

Query= curated2:Q58456
         (515 letters)



>FitnessBrowser__HerbieS:HSERO_RS21005
          Length = 623

 Score =  228 bits (580), Expect = 6e-64
 Identities = 159/482 (32%), Positives = 244/482 (50%), Gaps = 52/482 (10%)

Query: 1   MCGINGIIRF-GKEVIKEEINKMNKAIKHRGPDDEGIFIYNFKNYSIGLGHVRLAILDLS 59
           MCGI G+I F G  V  E + +M  AI HRGPD EG +I      ++GLGH RL+I+DLS
Sbjct: 1   MCGITGLINFDGSPVAPEVLKRMTNAIMHRGPDGEGHWIEG----NVGLGHRRLSIIDLS 56

Query: 60  EKGHQPMGYNVDEDKIIYRDDELDRADIIIVYNGEIYNYLELK---EKFNLETETGTDTE 116
             GHQPM         I  D        ++ YNGEIYNY EL+   E       + TDTE
Sbjct: 57  SAGHQPM---------ISTDHRF-----LLTYNGEIYNYRELRTELEALGYWFRSQTDTE 102

Query: 117 VILKLYNKLGFDCVKEFNGMWAFCIFDKKKGLIFCSRDRLGVKPFYYYWDGNEFIFSSEL 176
           V+L      G D +  FNGM+A  ++D+K+  +  +RDR G+KP YY        F SE 
Sbjct: 103 VVLHALECWGRDALLRFNGMFALALWDRKERELLLARDRYGIKPLYYARQAGCLAFGSEQ 162

Query: 177 KGILAVKEINKKENINKDAVELYFALGFIPSPYSIYKNTFKLEARQNLIFDLDKREIRKY 236
           K I AV    +K  ++  A+  YF    I +  ++ ++   L A    +    + +++ +
Sbjct: 163 KAITAVPAFQRK--LDLPALLEYFTFQNIFTDRTLLEDVRILPAGHYAVLKQGQNDLKLF 220

Query: 237 YYWELPDYKP--IYDKKKLIEEGKKLLYDAVKIRMRSDVPVGAFLSGGLDSSTVVGVMRE 294
            YW+    +P    DK+  +EE  +L   AV  ++ SDV +GA+LSGG+DS ++  +  +
Sbjct: 221 RYWDYRFREPEVAADKQAYLEELDRLFKQAVNRQLVSDVELGAYLSGGMDSGSITAIAAK 280

Query: 295 FTDLSKLHTFSIGF--------EGKYDETPYIKIVVDYFKTQHHHYYFKERDFEELIDKY 346
                 L TF+ GF        E  +DE    + +   FKT+H+    K  D E  + + 
Sbjct: 281 --SFPNLKTFTCGFDLSSASGIELAFDERTKAEAMSARFKTEHYEMVLKAGDMERCLPRL 338

Query: 347 SWIYDEPFGDYSGFPTYKVSEMARKFVTVVLSGDGGDEVFGGY--MTHLNGYRMDFIRKL 404
           +W  +EP    S +P Y  +++A KFV VVLSG GGDE+FGGY    +      DF   +
Sbjct: 339 AWHLEEPRVGQS-YPNYYAAKLAGKFVKVVLSGSGGDELFGGYPWRYYRAAMSQDFEHYI 397

Query: 405 PKFL----RVVGSK------LPVKKDLNGIANLYLLKEAFRL---SLINPEEFYAESIKE 451
            ++     R+V ++       PVK+ ++G+    + ++ F     +L  PE++   S+  
Sbjct: 398 DQYYLYWQRLVDNRHLKQMFAPVKQQVDGVWTRDIFRDVFATHDNALDRPEDYINHSLYF 457

Query: 452 DA 453
           +A
Sbjct: 458 EA 459


Lambda     K      H
   0.322    0.144    0.434 

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: 799
Number of extensions: 49
Number of successful extensions: 8
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: 515
Length of database: 623
Length adjustment: 36
Effective length of query: 479
Effective length of database: 587
Effective search space:   281173
Effective search space used:   281173
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 (21.9 bits)
S2: 53 (25.0 bits)

Align candidate HSERO_RS21005 HSERO_RS21005 (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.26266.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.4e-142  459.8   0.0   5.6e-139  450.3   0.0    2.0  2  lcl|FitnessBrowser__HerbieS:HSERO_RS21005  HSERO_RS21005 asparagine synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS21005  HSERO_RS21005 asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.3   0.0  5.6e-139  5.6e-139       1     491 [.       2     506 ..       2     514 .. 0.87
   2 !    7.7   0.0   8.1e-05   8.1e-05     490     517 .]     528     555 ..     519     555 .. 0.91

  Alignments for each domain:
  == domain 1  score: 450.3 bits;  conditional E-value: 5.6e-139
                                  TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsn 67 
                                                Cgi+g+++ +   +   e +k+m++++ hRGPD+eg+w++    n++lghrRL+iidls++ +QP+ +
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005   2 CGITGLINFDGSPVA-PEVLKRMTNAIMHRGPDGEGHWIE---GNVGLGHRRLSIIDLSSAgHQPMIS 65 
                                                *********987555.69**********************...8**************9999****** PP

                                  TIGR01536  68 ek.evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkg 134
                                                ++ + ++++nGEIYN++eLr ele+ Gy F++++DtEV+L+a+e wg++++ r++GmFA+alwd+k++
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005  66 TDhRFLLTYNGEIYNYRELRTELEALGYWFRSQTDTEVVLHALECWGRDALLRFNGMFALALWDRKER 133
                                                **999*************************************************************** PP

                                  TIGR01536 135 elflaRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevke 202
                                                el+laRDr+GikPLYya+++g l+f+SE Ka++a+++++++ld  al e++t+q+  t++tl ++v+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005 134 ELLLARDRYGIKPLYYARQAGCLAFGSEQKAITAVPAFQRKLDLPALLEYFTFQNIFTDRTLLEDVRI 201
                                                ******************************************************999*********** PP

                                  TIGR01536 203 lepakal.....dgeekleeywevekee..vkeseeelveelrelledavkkrlvadvpvgvllSGGl 263
                                                l++++++     +++ kl +yw+ + +e  v++++++  eel++l+++av+++lv+dv++g++lSGG+
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005 202 LPAGHYAvlkqgQNDLKLFRYWDYRFREpeVAADKQAYLEELDRLFKQAVNRQLVSDVELGAYLSGGM 269
                                                ******99996655666666***99888779999********************************** PP

                                  TIGR01536 264 DSslvaaiakkeaksevktFsigfe.dsk.....dldeskaarkvadelgtehkevliseeevlkele 325
                                                DS +++aia+k ++ ++ktF+ gf+  s+     ++de + a+++++ + teh+e+++++ ++   l+
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005 270 DSGSITAIAAKSFP-NLKTFTCGFDlSSAsgielAFDERTKAEAMSARFKTEHYEMVLKAGDMERCLP 336
                                                **************.8********9544333333588889**************************** PP

                                  TIGR01536 326 evilaleeptairasiplyllsklarekgvkVvLsGeGaDElfgGYey.freakaeeale......lp 386
                                                ++ ++leep  + +s+p y ++kla +  vkVvLsG G+DElfgGY + + +a +++++e      + 
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005 337 RLAWHLEEPR-VGQSYPNYYAAKLAGKF-VKVVLSGSGGDELFGGYPWrYYRAAMSQDFEhyidqyYL 402
                                                *********9.999**************.*****************8546666777777734333322 PP

                                  TIGR01536 387 easelaekklllqaklak.eselkellkakleeelkekeelkkelkee.....seleellrldlelll 448
                                                + ++l  +++l  +++a  +++   ++ +++ +++  ++++      +      ++++ l+ +++++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005 403 YWQRLVDNRHLK-QMFAPvKQQVDGVWTRDIFRDVFATHDN------AldrpeDYINHSLYFEAKTFL 463
                                                222222222222.3333303333344444444444443333......1233348999*********** PP

                                  TIGR01536 449 sdllrakDrvsmahslEvRvPflDkelvelalsippelklrdg 491
                                                ++l  ++D++smah+lE+RvPf+D++lv++a++ p++lkl++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005 464 HGLFVVEDKLSMAHGLESRVPFMDNDLVDFAMQCPVNLKLNNL 506
                                                ***************************************9975 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 8.1e-05
                                  TIGR01536 490 dgkeKvlLreaaeellPeeileRkKeaf 517
                                                 ++ K lLr ++++++P+++ + +K++f
  lcl|FitnessBrowser__HerbieS:HSERO_RS21005 528 TNDGKQLLRDMMARYIPDDVTKAEKQGF 555
                                                6889**********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (623 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 0.02s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 11.37
//
[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