Alignments for a candidate for gabT in Geotalea uraniireducens Rf4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Geotalea uraniireducens Rf4

Align Probable 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_011937064.1 GURA_RS00600 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_000016745.1:WP_011937064.1
          Length = 438

 Score =  409 bits (1051), Expect = e-119
 Identities = 202/420 (48%), Positives = 283/420 (67%)

Query: 15  QKRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKR 74
           Q ++Q V +GV+N + +   K  GA + D+DGR  IDFAG IG  NVGH HPKVV A+K 
Sbjct: 10  QLKNQHVPQGVANLSPAFISKARGAIMVDVDGRELIDFAGGIGVNNVGHCHPKVVAAIKD 69

Query: 75  QAEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKR 134
           QAE+ IH  F+V +Y  Y+ELA +L  +APG   K  +F NSGAEA ENA+KIAR  TKR
Sbjct: 70  QAEKYIHTCFHVALYEPYVELAARLNELAPGDFAKMTMFANSGAEADENAIKIARYATKR 129

Query: 135 QGVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDD 194
             V++F  GFHGRT MTM++TSKVKPYK G+GPFAPE Y+ P+ Y Y+ P GM+  +   
Sbjct: 130 PAVIAFENGFHGRTLMTMTLTSKVKPYKLGYGPFAPETYRIPYAYCYRCPFGMTYPACKA 189

Query: 195 MVIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEI 254
                  +FFI  VA E  A ++ EP+QGEGGFI P   +   + + C+++GI+ + DEI
Sbjct: 190 SCADYLEEFFINHVAAEQTAAIIAEPIQGEGGFITPPPEYFAKLQAICQKYGILLIIDEI 249

Query: 255 QTGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGGTYAGS 314
           QTG  RTG  FAI+H+ + PDLIT +KSLA G+PLS + GRAE+++ +  G LGGTY G+
Sbjct: 250 QTGMGRTGKIFAIDHWGIKPDLITTAKSLAGGMPLSAITGRAELMNMSHAGGLGGTYGGN 309

Query: 315 PLGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVK 374
           P+ C AALAVL+I+ E+GL  +++E+G  +  +  E ++    IG++R  G M A+E+V+
Sbjct: 310 PISCRAALAVLEILLEDGLLNKADELGAKLTARFEELQKTHEIIGEVRGKGPMLALELVR 369

Query: 375 DPDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILEAGL 434
           D +T+EP   +A  +     + GL++L+ G +GN+IR L PLVI+D  L  G++IL+  L
Sbjct: 370 DRETKEPAGAEAKKLTKLCFEKGLVILSCGNHGNVIRVLMPLVITDEELGRGIAILDESL 429


Lambda     K      H
   0.319    0.136    0.393 

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: 500
Number of extensions: 20
Number of successful extensions: 1
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: 436
Length of database: 438
Length adjustment: 32
Effective length of query: 404
Effective length of database: 406
Effective search space:   164024
Effective search space used:   164024
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: 51 (24.3 bits)

Align candidate WP_011937064.1 GURA_RS00600 (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.344069.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-170  552.8   0.2   2.3e-170  552.6   0.2    1.0  1  NCBI__GCF_000016745.1:WP_011937064.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016745.1:WP_011937064.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  552.6   0.2  2.3e-170  2.3e-170       3     419 ..      12     430 ..      10     431 .. 0.98

  Alignments for each domain:
  == domain 1  score: 552.6 bits;  conditional E-value: 2.3e-170
                             TIGR00700   3 raaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpy 75 
                                           +++ v++Gv++  + ++ ka ga++ dvdG++lid+a+gi+v nvGh hPkvv+a+k q+e+++ht+f+v  y
  NCBI__GCF_000016745.1:WP_011937064.1  12 KNQHVPQGVANLSPAFISKARGAIMVDVDGRELIDFAGGIGVNNVGHCHPKVVAAIKDQAEKYIHTCFHVALY 84 
                                           6799********************************************************************* PP

                             TIGR00700  76 esyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPyk 148
                                           e yvela +ln++aPg   k +++ nsGaea ena+kiar  t+rp+v+af++gfhGrt +tm+lt+kvkPyk
  NCBI__GCF_000016745.1:WP_011937064.1  85 EPYVELAARLNELAPGDFAKMTMFANSGAEADENAIKIARYATKRPAVIAFENGFHGRTLMTMTLTSKVKPYK 157
                                           ************************************************************************* PP

                             TIGR00700 149 iGfGPfapevyraPlpydyrdialdkqesldd.elaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                           +G+GPfape yr+P++y yr + +++  + +    + +e++f+  v+aeq aa++ eP+qGeGGfi p+ e+ 
  NCBI__GCF_000016745.1:WP_011937064.1 158 LGYGPFAPETYRIPYAYCYRCPFGMTYPACKAsCADYLEEFFINHVAAEQTAAIIAEPIQGEGGFITPPPEYF 230
                                           **************************999998456789*********************************** PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                           a+++ +c++ gi+li de+qtG+ rtGk+fai+h++ kPdlit+aksla+G+Pls+++Grae+++ +++GglG
  NCBI__GCF_000016745.1:WP_011937064.1 231 AKLQAICQKYGILLIIDEIQTGMGRTGKIFAIDHWGIKPDLITTAKSLAGGMPLSAITGRAELMNMSHAGGLG 303
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdtteP 365
                                           Gty+GnP+++ aalavl+i+ e+gl ++a+++g  ++ +  el+++ + ig+vrg+G m+a+elv d +t+eP
  NCBI__GCF_000016745.1:WP_011937064.1 304 GTYGGNPISCRAALAVLEILLEDGLLNKADELGAKLTARFEELQKTHEIIGEVRGKGPMLALELVrDRETKEP 376
                                           *****************************************************************9******* PP

                             TIGR00700 366 daalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                             a a+k+++   ++Gl++l++G +Gn+ir+l+Pl+i+de l  g+ il ++l 
  NCBI__GCF_000016745.1:WP_011937064.1 377 AGAEAKKLTKLCFEKGLVILSCGNHGNVIRVLMPLVITDEELGRGIAILDESLH 430
                                           *************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (438 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: 22.47
//
[ok]

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

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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