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_RS21370 RR42_RS21370 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Cup4G11:RR42_RS21370
          Length = 420

 Score =  593 bits (1528), Expect = e-174
 Identities = 292/419 (69%), Positives = 341/419 (81%), Gaps = 1/419 (0%)

Query: 3   MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62
           MKN EL +R+  ATPRGVGVMC+F+A+RAEN+ +WDVEG+ Y DFAAGIAVLNTGHRHPR
Sbjct: 1   MKNAELVRRKDAATPRGVGVMCNFFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPR 60

Query: 63  VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122
           +++A+  QLERFTHTAYQIVPY  Y+ LAERIN   P +G  KTA FTTGAEAVENAIKI
Sbjct: 61  LVEAMQRQLERFTHTAYQIVPYASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKI 120

Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182
           ARA TGRPGVIAFSG FHGRT++GMALTGKV PYK+GFGPFP +++HAP+P ALHGVS E
Sbjct: 121 ARAATGRPGVIAFSGGFHGRTMMGMALTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSVE 180

Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242
            AL+A+E LFK D+DP RVAAII EPVQGEGGF  AP  F++ LRA+CD+HGI+L+ADEV
Sbjct: 181 DALKAMEHLFKADVDPKRVAAIIFEPVQGEGGFNVAPPAFVKALRAICDEHGILLVADEV 240

Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302
           QTGFGRTGK+FAM H+DV PDL TMAKSLAGGMPLSAV GRA +MDAP PGGLGGTYAGN
Sbjct: 241 QTGFGRTGKLFAMEHYDVAPDLTTMAKSLAGGMPLSAVCGRAEVMDAPAPGGLGGTYAGN 300

Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362
           PLAVA+A AV+DV+E E+L  R A+LGQ+L   L A +   P +AE+RGLG+MVA EF  
Sbjct: 301 PLAVASALAVLDVLEGEQLIPRGAALGQRLVARLEALKARVPQIAEIRGLGAMVAVEF-R 359

Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421
            A G P AE  + VQ RALE GL+LL+CG YGNVIRFL+PLTI  A  +  L +L   L
Sbjct: 360 RADGAPDAEFTREVQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILADVL 418


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: 615
Number of extensions: 13
Number of successful extensions: 2
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: 420
Length adjustment: 32
Effective length of query: 391
Effective length of database: 388
Effective search space:   151708
Effective search space used:   151708
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: 50 (23.9 bits)

Align candidate RR42_RS21370 RR42_RS21370 (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.29560.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-195  635.5   1.7   1.8e-195  635.3   1.7    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS21370  RR42_RS21370 4-aminobutyrate ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS21370  RR42_RS21370 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  635.3   1.7  1.8e-195  1.8e-195       2     419 ..       9     419 ..       8     420 .] 0.99

  Alignments for each domain:
  == domain 1  score: 635.3 bits;  conditional E-value: 1.8e-195
                                 TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtaf 70 
                                               r++aa+++Gvgv+++++a +ae++e+ dv+G+r+id+aagiavln+Gh+hP++vea++rq+e++thta+
  lcl|FitnessBrowser__Cup4G11:RR42_RS21370   9 RKDAATPRGVGVMCNFFAERAENSEIWDVEGKRYIDFAAGIAVLNTGHRHPRLVEAMQRQLERFTHTAY 77 
                                               889****************************************************************** PP

                                 TIGR00700  71 qvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltma 139
                                               q+vpy sy+elae++n+ aPg g kk++++++Gaeavena+kiar+ tgrpgv+afs+gfhGrt + ma
  lcl|FitnessBrowser__Cup4G11:RR42_RS21370  78 QIVPYASYIELAERINQRAPGRGAKKTAFFTTGAEAVENAIKIARAATGRPGVIAFSGGFHGRTMMGMA 146
                                               ********************************************************************* PP

                                 TIGR00700 140 ltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqG 208
                                               lt+kv Pyk+GfGPf++ev++aP+p  +++ ++      +d l+a+e+lf+adv++++vaa+++ePvqG
  lcl|FitnessBrowser__Cup4G11:RR42_RS21370 147 LTGKVVPYKVGFGPFPGEVFHAPYPCALHGVSV------EDALKAMEHLFKADVDPKRVAAIIFEPVQG 209
                                               *****************************9988......66778************************* PP

                                 TIGR00700 209 eGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgv 277
                                               eGGf+v++  +v+a++ +c+ehgi+l+adevqtGf rtGklfa+eh+d+ Pdl t+aksla+G+Pls+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS21370 210 EGGFNVAPPAFVKALRAICDEHGILLVADEVQTGFGRTGKLFAMEHYDVAPDLTTMAKSLAGGMPLSAV 278
                                               ********************************************************************* PP

                                 TIGR00700 278 vGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdv 346
                                                Grae++dapapGglGGtyaGnPlava+alavld++e e li r   +g+++  +l  lk+ vp+i+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS21370 279 CGRAEVMDAPAPGGLGGTYAGNPLAVASALAVLDVLEGEQLIPRGAALGQRLVARLEALKARVPQIAEI 347
                                               ********************************************************************* PP

                                 TIGR00700 347 rglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkile 415
                                               rglGam+ave+  +d + Pda  +++++++al++Gllll++G++Gn+ir+l Pltisd+ ++egl+il 
  lcl|FitnessBrowser__Cup4G11:RR42_RS21370 348 RGLGAMVAVEFRRAD-GAPDAEFTREVQNRALEQGLLLLSCGVYGNVIRFLFPLTISDAVMNEGLDILA 415
                                               ***********9988.57*************************************************** PP

                                 TIGR00700 416 aala 419
                                               ++l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS21370 416 DVLT 419
                                               9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (420 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: 00:00:00.01
# Mc/sec: 10.59
//
[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