Alignments for a candidate for gabT in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Azospirillum brasilense Sp245

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__azobra:AZOBR_RS19630
          Length = 428

 Score =  541 bits (1395), Expect = e-158
 Identities = 269/424 (63%), Positives = 325/424 (76%), Gaps = 3/424 (0%)

Query: 3   MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62
           M N     RR  A PRG+      Y DRAENA LWDVEG  + DFA GIAVLNTGHRHP+
Sbjct: 1   MSNQSFQDRRNAAVPRGLANAMPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPK 60

Query: 63  VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122
           +++A+ AQL+RFTHT   + PY+ +VTLAER+NALVP     KTA FTTGAEAVENA+KI
Sbjct: 61  IIEAVKAQLDRFTHTCAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKI 120

Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182
           ARAHTGRPGVIAFSGAFHGRTLL MALTGKV PYK+GFGPFP+++YHAPFP+A  GVS +
Sbjct: 121 ARAHTGRPGVIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQ 180

Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242
            +L+ALE LFK+D+D  RVAAIIVEPVQGEGGF  AP +F++ LR +CD++GI+LI DE+
Sbjct: 181 DSLKALEQLFKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEI 240

Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302
           QTGF RTGKMFA+ H  VEPDL+TMAKSLAGG PLSAV+G+A IMDAP+PGG+GGTYAG+
Sbjct: 241 QTGFARTGKMFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGS 300

Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQL--REHLLAQRKHCPAMAEVRGLGSMVAAEF 360
           PLA  AA AV+DVIEEEKL +RS  LG+++  R   +AQR     + +VR LG M+A E 
Sbjct: 301 PLATTAALAVLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMEL 360

Query: 361 C-DPATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQ 419
             D  T +P+AE  K +  +A E GLVLL+CGTYGNVIR L PLT   A  D  L ++ +
Sbjct: 361 VKDRGTKEPAAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIER 420

Query: 420 ALAE 423
           +L E
Sbjct: 421 SLEE 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: 587
Number of extensions: 18
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: 428
Length adjustment: 32
Effective length of query: 391
Effective length of database: 396
Effective search space:   154836
Effective search space used:   154836
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 AZOBR_RS19630 AZOBR_RS19630 (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.17180.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.7e-194  630.0   2.1     9e-194  629.8   2.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS19630  AZOBR_RS19630 4-aminobutyrate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS19630  AZOBR_RS19630 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.8   2.1    9e-194    9e-194       2     419 ..       9     423 ..       8     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 629.8 bits;  conditional E-value: 9e-194
                                 TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtaf 70 
                                               rr+aav++G++++++v++ +ae+ael dv+Gnr+id+a+giavln+Gh+hPk++eavk q++++tht+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS19630   9 RRNAAVPRGLANAMPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHTCA 77 
                                               9******************************************************************** PP

                                 TIGR00700  71 qvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltma 139
                                               +v+pyes+v+lae+lna+ Pgs +kk++++++Gaeavenavkiar++tgrpgv+afs++fhGrt l+ma
  lcl|FitnessBrowser__azobra:AZOBR_RS19630  78 MVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGAFHGRTLLAMA 146
                                               ********************************************************************* PP

                                 TIGR00700 140 ltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqG 208
                                               lt+kv Pyk+GfGPf++evy+aP+p  yr+ ++  q+sl+    a+e+lf++dv+a +vaa+++ePvqG
  lcl|FitnessBrowser__azobra:AZOBR_RS19630 147 LTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSV--QDSLK----ALEQLFKSDVDATRVAAIIVEPVQG 209
                                               ******************************999..66665....************************* PP

                                 TIGR00700 209 eGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgv 277
                                               eGGf++++ e+++a++++c+e+gi+li de+qtGfartGk+faieh +++Pdl+t+aksla+G+Pls+v
  lcl|FitnessBrowser__azobra:AZOBR_RS19630 210 EGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGKMFAIEHSGVEPDLMTMAKSLAGGFPLSAV 278
                                               ********************************************************************* PP

                                 TIGR00700 278 vGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdkliel..keevpaig 344
                                               +G+aei+dap pGg+GGtyaG+Pla +aalavld+ieee li+r++++g+++  +  ++  +++  +ig
  lcl|FitnessBrowser__azobra:AZOBR_RS19630 279 TGKAEIMDAPIPGGIGGTYAGSPLATTAALAVLDVIEEEKLIQRSNDLGERIAGRFRTMaqRNTLSVIG 347
                                               ****************************************************998876611567789** PP

                                 TIGR00700 345 dvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglk 412
                                               dvr+lG mia+elv d +t+eP a l++++ a+a ++Gl+ll++G +Gn+ir+l Plt sd+l+degl+
  lcl|FitnessBrowser__azobra:AZOBR_RS19630 348 DVRNLGGMIAMELVkDRGTKEPAAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLD 416
                                               **************999**************************************************** PP

                                 TIGR00700 413 ileaala 419
                                               i+e +l+
  lcl|FitnessBrowser__azobra:AZOBR_RS19630 417 IIERSLE 423
                                               **99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (428 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: 7.36
//
[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