Alignments for a candidate for gabT in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Rhizorhabdus wittichii RW1

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_012050389.1 SWIT_RS21305 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_000016765.1:WP_012050389.1
          Length = 425

 Score =  492 bits (1267), Expect = e-144
 Identities = 246/421 (58%), Positives = 308/421 (73%), Gaps = 3/421 (0%)

Query: 5   NLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVM 64
           N +L  RR  A  RGV      +A RA+NA +WDV+G+ Y DFA GIAVLNTGHRHP+V+
Sbjct: 4   NADLLARRRQAVARGVATAFPIFAARADNAEIWDVDGQHYVDFAGGIAVLNTGHRHPKVI 63

Query: 65  QAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIAR 124
            A+  QL  +TH A+Q+  Y+ YV LAER+NAL P  G  KT LFTTGAEA ENA+K+AR
Sbjct: 64  AAVQEQLALYTHMAFQVAAYEPYVALAERLNALAPFTGEAKTILFTTGAEATENAVKLAR 123

Query: 125 AHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERA 184
           A TGR  VIAF G FHGRTLL MA+TGKVAPYK  FGP P +I+H PFP A HG S E  
Sbjct: 124 AATGRSAVIAFGGGFHGRTLLAMAMTGKVAPYKQQFGPMPGEIFHVPFPVAAHGGSVEET 183

Query: 185 LQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQT 244
           L+A+E +F+  ++P RVAA+I+EP+ GEGGF  AP + +R LRA+CD+HGI+LIADEVQT
Sbjct: 184 LRAIEMVFRVAVEPGRVAALIIEPILGEGGFYEAPVELLRALRALCDRHGIILIADEVQT 243

Query: 245 GFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPL 304
           GFGRTG+MFA+ H  VEPDL+T+AKSLAGG PLS V GR+AIM+A  PGG+GGTY GNP+
Sbjct: 244 GFGRTGRMFAIEHSGVEPDLVTVAKSLAGGFPLSGVIGRSAIMEASEPGGMGGTYGGNPV 303

Query: 305 AVAAAHAVIDVIEEEKLCERSASLGQQLRE--HLLAQRKHCPAMAEVRGLGSMVAAEFCD 362
           A AAA AV+DVI EE+L +R+ ++G +++E   LLA+R     + E+RG G+M+  +   
Sbjct: 304 ACAAALAVLDVIAEEQLLDRAVAIGARIKERLRLLARRNDLVPITEIRGPGAMIGFDIVT 363

Query: 363 PATG-QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421
             TG +P  E  +RV   A EAGL+LL+CG +GNVIR L PLT+P    DA LA L QAL
Sbjct: 364 SRTGYEPDPETTRRVVEAAREAGLILLSCGIHGNVIRILVPLTVPDDILDAGLAKLEQAL 423

Query: 422 A 422
           A
Sbjct: 424 A 424


Lambda     K      H
   0.321    0.136    0.400 

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: 610
Number of extensions: 34
Number of successful extensions: 3
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: 423
Length of database: 425
Length adjustment: 32
Effective length of query: 391
Effective length of database: 393
Effective search space:   153663
Effective search space used:   153663
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: 51 (24.3 bits)

Align candidate WP_012050389.1 SWIT_RS21305 (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.3747720.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.8e-170  550.9   6.2   8.8e-170  550.7   6.2    1.0  1  NCBI__GCF_000016765.1:WP_012050389.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_012050389.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.7   6.2  8.8e-170  8.8e-170       2     419 ..      10     424 ..       9     425 .] 0.97

  Alignments for each domain:
  == domain 1  score: 550.7 bits;  conditional E-value: 8.8e-170
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           rr +av++Gv+++ +++aa+a++ae+ dvdG++++d+a+giavln+Gh+hPkv++av++q++ +th afqv  
  NCBI__GCF_000016765.1:WP_012050389.1  10 RRRQAVARGVATAFPIFAARADNAEIWDVDGQHYVDFAGGIAVLNTGHRHPKVIAAVQEQLALYTHMAFQVAA 82 
                                           89*********************************************************************** PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye yv+lae+lna+aP +ge+k++l+++Gaea enavk+ar+ tgr +v+af +gfhGrt l+ma+t+kv+Py
  NCBI__GCF_000016765.1:WP_012050389.1  83 YEPYVALAERLNALAPFTGEAKTILFTTGAEATENAVKLARAATGRSAVIAFGGGFHGRTLLAMAMTGKVAPY 155
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                           k  fGP+++e++++P+p   +++++      ++ l+aie +f + ve+ +vaa+++eP+ GeGGf  ++ el+
  NCBI__GCF_000016765.1:WP_012050389.1 156 KQQFGPMPGEIFHVPFPVAAHGGSV------EETLRAIEMVFRVAVEPGRVAALIIEPILGEGGFYEAPVELL 222
                                           *******************999987......66788************************************* PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                            a++ lc++hgi+liadevqtGf rtG++faieh +++Pdl+tvaksla+G+Plsgv+Gr+ i++a++pGg+G
  NCBI__GCF_000016765.1:WP_012050389.1 223 RALRALCDRHGIILIADEVQTGFGRTGRMFAIEHSGVEPDLVTVAKSLAGGFPLSGVIGRSAIMEASEPGGMG 295
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevp..aigdvrglGamiavelvdpdtt. 363
                                           Gty+GnP+a+aaalavld+i ee l +ra  ig ++k++l  l +  +   i+++rg Gami  ++v + t+ 
  NCBI__GCF_000016765.1:WP_012050389.1 296 GTYGGNPVACAAALAVLDVIAEEQLLDRAVAIGARIKERLRLLARRNDlvPITEIRGPGAMIGFDIVTSRTGy 368
                                           **************************************98766555441169***************999866 PP

                             TIGR00700 364 ePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                           ePd   ++++ +aa++aGl+ll++Gi+Gn+ir+l Plt++d++ld+gl  le+ala
  NCBI__GCF_000016765.1:WP_012050389.1 369 EPDPETTRRVVEAAREAGLILLSCGIHGNVIRILVPLTVPDDILDAGLAKLEQALA 424
                                           ****************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (425 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 21.77
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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