Alignments for a candidate for gabT in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Cupriavidus basilensis 4G11

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Cup4G11:RR42_RS26160
          Length = 424

 Score =  719 bits (1856), Expect = 0.0
 Identities = 354/420 (84%), Positives = 383/420 (91%)

Query: 3   MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62
           MKNLELNQRR LATPRGVGVMCDFYADRAENATLWDVEGR YTDFA GIAVLNTGHRHPR
Sbjct: 1   MKNLELNQRRALATPRGVGVMCDFYADRAENATLWDVEGRQYTDFACGIAVLNTGHRHPR 60

Query: 63  VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122
           VMQA+ AQLERFTHTAYQIVPY+ YV LAERINALVPI GL KTALFTTGAEAVENA+KI
Sbjct: 61  VMQAVIAQLERFTHTAYQIVPYESYVALAERINALVPIDGLKKTALFTTGAEAVENAVKI 120

Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182
           ARAHTGRPGVIAFSG FHGRTLLGMALTGKVAPYK+GFGPFPSDIYHAPFP  LHGVSTE
Sbjct: 121 ARAHTGRPGVIAFSGGFHGRTLLGMALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTE 180

Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242
           +++QALE LFKTDIDP RVAAII+EPVQGEGGF  AP DFM+ LRA+CD+HGI+LIADEV
Sbjct: 181 QSIQALESLFKTDIDPQRVAAIIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEV 240

Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302
           QTGFGRTGK+FAMSH+ V PDLITMAKSLAGGMPLSAV GRA+IMDAPLPGGLGGTYAGN
Sbjct: 241 QTGFGRTGKLFAMSHYPVAPDLITMAKSLAGGMPLSAVCGRASIMDAPLPGGLGGTYAGN 300

Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362
           PLAVAAAHAVI+ IE+E+LCER+ +LG+QL+  L    + CP +A++RGLGSMVA EF D
Sbjct: 301 PLAVAAAHAVIETIEQERLCERATALGKQLKAALQQASQTCPGIADIRGLGSMVAVEFHD 360

Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
           PATGQPSAE AKRVQ RA+EAGL+LLTCGTYGN IRFLYPLTIPQAQFDAAL VLT+ LA
Sbjct: 361 PATGQPSAELAKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVLTKVLA 420


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: 718
Number of extensions: 21
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: 423
Length of database: 424
Length adjustment: 32
Effective length of query: 391
Effective length of database: 392
Effective search space:   153272
Effective search space used:   153272
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 RR42_RS26160 RR42_RS26160 (4-aminobutyrate aminotransferase)
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.4410.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-195  634.4   1.0   3.9e-195  634.2   1.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS26160  RR42_RS26160 4-aminobutyrate ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS26160  RR42_RS26160 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  634.2   1.0  3.9e-195  3.9e-195       1     419 [.       8     420 ..       8     421 .. 0.99

  Alignments for each domain:
  == domain 1  score: 634.2 bits;  conditional E-value: 3.9e-195
                                 TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthta 69 
                                               qrra a+++Gvgv+++++a +ae+a+l dv+G+++ d+a+giavln+Gh+hP+v++av  q+e++thta
  lcl|FitnessBrowser__Cup4G11:RR42_RS26160   8 QRRALATPRGVGVMCDFYADRAENATLWDVEGRQYTDFACGIAVLNTGHRHPRVMQAVIAQLERFTHTA 76 
                                               79******************************************************************* PP

                                 TIGR00700  70 fqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltm 138
                                               +q+vpyesyv+lae++na+ P  g kk++l+++Gaeavenavkiar++tgrpgv+afs+gfhGrt l m
  lcl|FitnessBrowser__Cup4G11:RR42_RS26160  77 YQIVPYESYVALAERINALVPIDGLKKTALFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTLLGM 145
                                               ********************************************************************* PP

                                 TIGR00700 139 altakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvq 207
                                               alt+kv+Pyk+GfGPf++++y+aP+p d+++ ++      ++ ++a+e+lf++d+++++vaa+++ePvq
  lcl|FitnessBrowser__Cup4G11:RR42_RS26160 146 ALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVST------EQSIQALESLFKTDIDPQRVAAIIIEPVQ 208
                                               *******************************998......45678************************ PP

                                 TIGR00700 208 GeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsg 276
                                               GeGGf  ++ +++++++ lc++hgi+liadevqtGf rtGklfa+ h+ + Pdlit+aksla+G+Pls+
  lcl|FitnessBrowser__Cup4G11:RR42_RS26160 209 GEGGFHPAPVDFMQTLRALCDKHGILLIADEVQTGFGRTGKLFAMSHYPVAPDLITMAKSLAGGMPLSA 277
                                               ********************************************************************* PP

                                 TIGR00700 277 vvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigd 345
                                               v Gra i+dap pGglGGtyaGnPlavaaa+av+++ie+e l+era  +gk +k  l ++ ++ p i+d
  lcl|FitnessBrowser__Cup4G11:RR42_RS26160 278 VCGRASIMDAPLPGGLGGTYAGNPLAVAAAHAVIETIEQERLCERATALGKQLKAALQQASQTCPGIAD 346
                                               ********************************************************************* PP

                                 TIGR00700 346 vrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkil 414
                                               +rglG+m+ave+ dp t++P+a la++++ +a +aGl+llt+G +Gn ir+l+Plti+ +++d++l +l
  lcl|FitnessBrowser__Cup4G11:RR42_RS26160 347 IRGLGSMVAVEFHDPATGQPSAELAKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVL 415
                                               ********************************************************************* PP

                                 TIGR00700 415 eaala 419
                                               +++la
  lcl|FitnessBrowser__Cup4G11:RR42_RS26160 416 TKVLA 420
                                               99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (424 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.41
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 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