Alignments for a candidate for gabT in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudarthrobacter sulfonivorans Ar51

Align 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_058931602.1 AU252_RS16125 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P63505
         (449 letters)



>NCBI__GCF_001484605.1:WP_058931602.1
          Length = 456

 Score =  553 bits (1426), Expect = e-162
 Identities = 284/448 (63%), Positives = 344/448 (76%), Gaps = 12/448 (2%)

Query: 4   LQQSRRLVTEIPGPASQALTHRRAAAVSSGVGVTLPVFVARAGGGIVEDVDGNRLIDLGS 63
           L+Q RR+  + PGP S ALT RR A V++GV   +PV+VA A GGI+ DVDGN  IDLGS
Sbjct: 12  LEQKRRVQADFPGPKSIALTERRKAVVAAGVASAVPVYVADADGGIIHDVDGNSFIDLGS 71

Query: 64  GIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPYEGYVAVAEQLNRITPGSGPKRSVLF 123
           GIAVT++G S P VV AV+  V  FTHTCFMVTPYE YVA+AEQLNR+TPG   KR+VLF
Sbjct: 72  GIAVTSVGASDPAVVGAVKEAVEHFTHTCFMVTPYESYVALAEQLNRLTPGDHEKRTVLF 131

Query: 124 NSGAEAVENAVKIARSYTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYR 183
           NSGAEAVENAVK+AR  TG+ AVVAFDHAYHGRTNLTMALTAK+MPYK+ FGPFAPE+YR
Sbjct: 132 NSGAEAVENAVKVARLATGRDAVVAFDHAYHGRTNLTMALTAKAMPYKTNFGPFAPEVYR 191

Query: 184 APLSYPYRDGLLDKQLATNGELAAARAIGVIDKQVGANNLAALVIEPIQGEGGFIVPAEG 243
            P+SYP+R    ++  +  G  AA RAI +I+KQ+G + +AA++IEPIQGEGGFIVPAEG
Sbjct: 192 MPMSYPFR----EENPSITGAEAAKRAITMIEKQIGGDQVAAIIIEPIQGEGGFIVPAEG 247

Query: 244 FLPALLDWCRKNHVVFIADEVQTGFARTGAMFACEHEGPDGLEPDLICTAKGIADGLPLS 303
           FLPAL  W + N VVFIADEVQ+GF RTG  FA  HE    + PD+I  AKGIA G+PLS
Sbjct: 248 FLPALAAWAKTNGVVFIADEVQSGFCRTGEWFAVNHE---DVVPDIITMAKGIAGGMPLS 304

Query: 304 AVTGRAEIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERARQIERLVTDRLTT 363
           A+TGRA++++A H GGLGGT+GGNPVACAAALA I ++E   L  RAR IE L T RL  
Sbjct: 305 AITGRADLLDAVHPGGLGGTYGGNPVACAAALAAIGSMEEYNLAGRARHIESLATGRLQE 364

Query: 364 LQAV-----DDRIGDVRGRGAMIAVELVKSGTTEPDAGLTERLATAAHAAGVIILTCGMF 418
           LQA         IGD+RGRGAM+AVELV++G+ EP+  LT+ +A A    GVIILTCG +
Sbjct: 365 LQAELAGAGKSVIGDIRGRGAMLAVELVQAGSKEPNPELTKAVAAACLKEGVIILTCGTY 424

Query: 419 GNIIRLLPPLTIGDELLSEGLDIVCAIL 446
           GN+IRLLPPL I D+LL++GLD++ A +
Sbjct: 425 GNVIRLLPPLVITDDLLNDGLDVLAAAI 452


Lambda     K      H
   0.319    0.137    0.397 

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: 640
Number of extensions: 24
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: 449
Length of database: 456
Length adjustment: 33
Effective length of query: 416
Effective length of database: 423
Effective search space:   175968
Effective search space used:   175968
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_058931602.1 AU252_RS16125 (4-aminobutyrate--2-oxoglutarate transaminase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

# 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.carbon/TIGR00700.hmm
# target sequence database:        /tmp/gapView.32466.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00700  [M=420]
Accession:   TIGR00700
Description: GABAtrnsam: 4-aminobutyrate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-183  594.2   7.9   6.3e-183  594.0   7.9    1.0  1  NCBI__GCF_001484605.1:WP_058931602.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001484605.1:WP_058931602.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.0   7.9  6.3e-183  6.3e-183       2     419 ..      33     453 ..      32     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 594.0 bits;  conditional E-value: 6.3e-183
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           rr+a+v+ Gv+ +++v++a a+g++++dvdGn +idl++giav++vG s+P vv avk+ ve++tht+f+v+p
  NCBI__GCF_001484605.1:WP_058931602.1  33 RRKAVVAAGVASAVPVYVADADGGIIHDVDGNSFIDLGSGIAVTSVGASDPAVVGAVKEAVEHFTHTCFMVTP 105
                                           99*********************************************************************** PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           yesyv+lae+ln+++Pg +ek++vl+nsGaeavenavk+ar  tgr++vvaf++++hGrtnltmaltak++Py
  NCBI__GCF_001484605.1:WP_058931602.1 106 YESYVALAEQLNRLTPGDHEKRTVLFNSGAEAVENAVKVARLATGRDAVVAFDHAYHGRTNLTMALTAKAMPY 178
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvad..veaeqvaavvlePvqGeGGfivpake 218
                                           k+ fGPfapevyr+P++y++r+       s+ +  aa +a+ +++  ++ +qvaa+++eP+qGeGGfivpa++
  NCBI__GCF_001484605.1:WP_058931602.1 179 KTNFGPFAPEVYRMPMSYPFREENP----SITGAEAAKRAITMIEkqIGGDQVAAIIIEPIQGEGGFIVPAEG 247
                                           *********************9877....666666788888777667************************** PP

                             TIGR00700 219 lvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGg 291
                                           +++a+a + k +g+v+iadevq+Gf rtG+ fa++hed++Pd+it+ak++a+G+Pls+++Gra++lda +pGg
  NCBI__GCF_001484605.1:WP_058931602.1 248 FLPALAAWAKTNGVVFIADEVQSGFCRTGEWFAVNHEDVVPDIITMAKGIAGGMPLSAITGRADLLDAVHPGG 320
                                           ************************************************************************* PP

                             TIGR00700 292 lGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkee.....vpaigdvrglGamiavelvd 359
                                           lGGty+GnP+a+aaala +  +ee  l+ ra++i+ l + +l el++e       +igd+rg+Gam+avelv+
  NCBI__GCF_001484605.1:WP_058931602.1 321 LGGTYGGNPVACAAALAAIGSMEEYNLAGRARHIESLATGRLQELQAElagagKSVIGDIRGRGAMLAVELVQ 393
                                           **********************************************9833332468***************** PP

                             TIGR00700 360 pdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                           ++++eP+  l++++aaa l++G+++lt+G +Gn+irll+Pl+i+d+ll++gl++l aa++
  NCBI__GCF_001484605.1:WP_058931602.1 394 AGSKEPNPELTKAVAAACLKEGVIILTCGTYGNVIRLLPPLVITDDLLNDGLDVLAAAIK 453
                                           *******************************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (456 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 23.56
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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 2024 update 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

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 catabolism of small carbon sources