Alignments for a candidate for gatB in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Crocosphaera subtropica ATCC 51142

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_009544472.1 CCE_RS07910 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_000017845.1:WP_009544472.1
          Length = 495

 Score =  556 bits (1433), Expect = e-163
 Identities = 277/487 (56%), Positives = 364/487 (74%), Gaps = 10/487 (2%)

Query: 69  DYEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVR 128
           +YEA+IG+ETH QL+T +K FC+CS  + S PNT++CP+C+G PG LPVLN +V+   V+
Sbjct: 10  EYEAIIGLETHCQLNTTSKIFCNCSTEFDSPPNTNVCPICLGYPGVLPVLNEEVLASAVK 69

Query: 129 LGLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGHRR-- 186
           LGLALN  ++  SKFDRKQYFYPDLPK YQISQFD+PI   G +++++  +      R  
Sbjct: 70  LGLALNAKIAPYSKFDRKQYFYPDLPKNYQISQFDLPIVEHGSLEIELVDKKSKEVTRKT 129

Query: 187 FGITRVHMEEDAGKLLHSDT-----GDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYAC 241
            GITR+HMEEDAGKL+H+ +       +S VD NR GVPLLEIVSEPD+RSG EAAEYA 
Sbjct: 130 IGITRLHMEEDAGKLVHAGSDRLAGSTHSLVDFNRTGVPLLEIVSEPDIRSGQEAAEYAQ 189

Query: 242 EMQRIARYLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEI 301
           E++R+ RYLG+S+GNMQEGSLRCDVNIS+RP+GQ EFGTKVEIKN+N+FSAI +AI++EI
Sbjct: 190 ELRRLVRYLGISDGNMQEGSLRCDVNISVRPVGQKEFGTKVEIKNMNSFSAIQKAIEYEI 249

Query: 302 SRQALLYNQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVD 361
            RQ      G  D I  ETRLW+E  Q+T++MRKKEG +DYRYFPEPDLP + +++E ++
Sbjct: 250 ERQIEAVENG--DPIYQETRLWDESNQETISMRKKEGSSDYRYFPEPDLPPLEVSEEKLN 307

Query: 362 SIRASLPELPEAKRRRYE-AMGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMS 420
           + +  LPELP  KR+RYE A+GL   D   L +D  VAEY++  +  GA+ KL ANW+  
Sbjct: 308 AWKQELPELPAQKRKRYEEALGLSAYDARVLTDDREVAEYYETAVNTGADAKLVANWVTQ 367

Query: 421 DIAAYLKNEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKA 480
           DIAAYL N KLSI +I L P  L EL+  I+ GTISGKI KEIL ELL KGG+ K ++++
Sbjct: 368 DIAAYLNNSKLSIIEIALKPDSLGELVQLIEKGTISGKIAKEILPELLEKGGSPKKIVES 427

Query: 481 KDLVQITDPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNK 540
           K + QI+DPAEIEK++  ++  NP ++E+YR GK KL+G+F GQVMK + G+A+P L N+
Sbjct: 428 KGMTQISDPAEIEKVIEALMEANPSEVEKYRGGKKKLKGFFVGQVMKETGGRADPKLTNQ 487

Query: 541 ILLEKLN 547
           +  + LN
Sbjct: 488 LAEKLLN 494


Lambda     K      H
   0.317    0.134    0.379 

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: 801
Number of extensions: 35
Number of successful extensions: 5
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: 550
Length of database: 495
Length adjustment: 35
Effective length of query: 515
Effective length of database: 460
Effective search space:   236900
Effective search space used:   236900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_009544472.1 CCE_RS07910 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

# 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.13685.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-209  680.3   0.0   7.1e-209  680.2   0.0    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009544472.1  CCE_RS07910 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009544472.1  CCE_RS07910 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  680.2   0.0  7.1e-209  7.1e-209       2     481 .]       9     494 ..       8     494 .. 0.99

  Alignments for each domain:
  == domain 1  score: 680.2 bits;  conditional E-value: 7.1e-209
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +eye++iGlE+H+qlnt sK+Fc+cs+e+++ +pNtnvcp+clg+PG+lPvlN+e++++A+kl+laln+
  lcl|NCBI__GCF_000017845.1:WP_009544472.1   9 TEYEAIIGLETHCQLNTTSKIFCNCSTEFDS-PPNTNVCPICLGYPGVLPVLNEEVLASAVKLGLALNA 76 
                                               79*****************************.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke......keigierlhlEeDtgks 133
                                               k ++++s+FdRK+YfYpDlPk+yqi+q+dlPi+e+G+leiel +k+      k+igi+rlh+EeD+gk+
  lcl|NCBI__GCF_000017845.1:WP_009544472.1  77 K-IAPYSKFDRKQYFYPDLPKNYQISQFDLPIVEHGSLEIELVDKKskevtrKTIGITRLHMEEDAGKL 144
                                               *.668************************************99998999******************** PP

                                 TIGR00133 134 qykesdk...dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvD 199
                                               ++++sd+   +++slvDfNR+gvPLlEiV++Pd++s++ea+++ ++lr+++ryl+isdg+++eGs+R+D
  lcl|NCBI__GCF_000017845.1:WP_009544472.1 145 VHAGSDRlagSTHSLVDFNRTGVPLLEIVSEPDIRSGQEAAEYAQELRRLVRYLGISDGNMQEGSLRCD 213
                                               ******99999********************************************************** PP

                                 TIGR00133 200 vNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkK 268
                                               vN+s+r++Gq+++gt+vEiKN+ns+++i+kaieyEieRq++++++g+ ++qetr +de+++ t+s+RkK
  lcl|NCBI__GCF_000017845.1:WP_009544472.1 214 VNISVRPVGQKEFGTKVEIKNMNSFSAIQKAIEYEIERQIEAVENGDPIYQETRLWDESNQETISMRKK 282
                                               ********************************************************************* PP

                                 TIGR00133 269 eeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafee 337
                                               e s+DYRYfpePdlpp+e++ee ++  ++++lpelP +kr+r+++ +gls++da+vl++d+e+++++e+
  lcl|NCBI__GCF_000017845.1:WP_009544472.1 283 EGSSDYRYFPEPDLPPLEVSEEKLNA-WKQELPELPAQKRKRYEEALGLSAYDARVLTDDREVAEYYET 350
                                               **********************9988.****************************************** PP

                                 TIGR00133 338 vvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkk 406
                                               +v++ +++kl++nW++++++++Ln++k+s+ e +lkp++l el++li++g+is+k+ake+l elle+++
  lcl|NCBI__GCF_000017845.1:WP_009544472.1 351 AVNTGADAKLVANWVTQDIAAYLNNSKLSIIEIALKPDSLGELVQLIEKGTISGKIAKEILPELLEKGG 419
                                               ********************************************************************* PP

                                 TIGR00133 407 dpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekl 475
                                               +pkk++e +g++qisd+ e+ k++e+ ++ np eveky+ gk+k+ +f+vGqvmk+t gradpk +++l
  lcl|NCBI__GCF_000017845.1:WP_009544472.1 420 SPKKIVESKGMTQISDPAEIEKVIEALMEANPSEVEKYRGGKKKLKGFFVGQVMKETGGRADPKLTNQL 488
                                               ********************************************************************* PP

                                 TIGR00133 476 lkells 481
                                                ++ll+
  lcl|NCBI__GCF_000017845.1:WP_009544472.1 489 AEKLLN 494
                                               999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (495 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: 00:00:00.03
# Mc/sec: 7.71
//
[ok]

This GapMind analysis is from Apr 10 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