Alignments for a candidate for gabT in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Herbaspirillum seropedicae SmR1

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__HerbieS:HSERO_RS05420
          Length = 426

 Score =  627 bits (1617), Expect = 0.0
 Identities = 305/423 (72%), Positives = 360/423 (85%), Gaps = 2/423 (0%)

Query: 1   MTMK--NLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGH 58
           MT K  N EL QR+  ATPRGVGVMCDFYA+RA NA LWDVEGR + DFAAGIAVLNTGH
Sbjct: 1   MTSKANNQELQQRKNAATPRGVGVMCDFYAERAANAELWDVEGRRFIDFAAGIAVLNTGH 60

Query: 59  RHPRVMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVEN 118
           RHP+++ A+ AQ+++FTHTAYQIVPY  YV LAERIN L P     KTA F+TGAEAVEN
Sbjct: 61  RHPKLLDAMRAQMDKFTHTAYQIVPYASYVELAERINRLTPGNYPKKTAFFSTGAEAVEN 120

Query: 119 AIKIARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHG 178
           AIKIARAHTGRPGVIAF+G FHGRT++GMALTGKVAPYK+GFGPFP D++HAP+PSALHG
Sbjct: 121 AIKIARAHTGRPGVIAFAGGFHGRTMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHG 180

Query: 179 VSTERALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLI 238
           +++E AL+A++GLFK+DI+  RVAAII+EPVQGEGGF AAPADFMRGLRA+CD+HGI+LI
Sbjct: 181 ITSEDALEAVKGLFKSDIEAKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLI 240

Query: 239 ADEVQTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGT 298
           ADEVQ+G+GRTGK+FAM H+DV PDL+TMAKSLAGGMPLSAV+GRA IMDAP PGGLGGT
Sbjct: 241 ADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGT 300

Query: 299 YAGNPLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAA 358
           YAGNPLA+A+A AV+DV+EEE+L  R   LG +L+EHL   R   P +AEVRG+G+MVA 
Sbjct: 301 YAGNPLAIASALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAV 360

Query: 359 EFCDPATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLT 418
           EF DPATG+P AE+ K+VQ  AL  GL+LLTCG+YGNVIRFL+PLTIP    D AL +L 
Sbjct: 361 EFADPATGKPDAEYTKKVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILA 420

Query: 419 QAL 421
           +A+
Sbjct: 421 KAI 423


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: 671
Number of extensions: 18
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: 426
Length adjustment: 32
Effective length of query: 391
Effective length of database: 394
Effective search space:   154054
Effective search space used:   154054
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 HSERO_RS05420 HSERO_RS05420 (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.7514.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.3e-197  640.7   0.4   5.2e-197  640.4   0.4    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05420  HSERO_RS05420 4-aminobutyrate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05420  HSERO_RS05420 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  640.4   0.4  5.2e-197  5.2e-197       1     418 [.      12     423 ..      12     425 .. 0.99

  Alignments for each domain:
  == domain 1  score: 640.4 bits;  conditional E-value: 5.2e-197
                                  TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveeltht 68 
                                                qr++aa+++Gvgv+++++a +a +ael dv+G+r+id+aagiavln+Gh+hPk+++a++ q++++tht
  lcl|FitnessBrowser__HerbieS:HSERO_RS05420  12 QRKNAATPRGVGVMCDFYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHT 79 
                                                7999**************************************************************** PP

                                  TIGR00700  69 afqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnl 136
                                                a+q+vpy syvelae++n+++Pg  +kk++++++Gaeavena+kiar++tgrpgv+af +gfhGrt +
  lcl|FitnessBrowser__HerbieS:HSERO_RS05420  80 AYQIVPYASYVELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIARAHTGRPGVIAFAGGFHGRTMM 147
                                                ******************************************************************** PP

                                  TIGR00700 137 tmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvle 204
                                                 malt+kv+Pyk+GfGPf+++v++aP+p+ +++i++  ++     l+a++ lf++d+ea++vaa++le
  lcl|FitnessBrowser__HerbieS:HSERO_RS05420 148 GMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITS--ED----ALEAVKGLFKSDIEAKRVAAIILE 209
                                                *********************************988..55....556********************* PP

                                  TIGR00700 205 PvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGl 272
                                                PvqGeGGf  ++ +++  ++ lc+ehgi+liadevq+G+ rtGklfa+eh+d+ Pdl+t+aksla+G+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05420 210 PVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKSLAGGM 277
                                                ******************************************************************** PP

                                  TIGR00700 273 PlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeev 340
                                                Pls+v Graei+dapapGglGGtyaGnPla+a+alavld++eee l+ r +++g  ++++l el+ +v
  lcl|FitnessBrowser__HerbieS:HSERO_RS05420 278 PLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSV 345
                                                ******************************************************************** PP

                                  TIGR00700 341 paigdvrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelld 408
                                                p+i++vrg Gam+ave+ dp t++Pda  ++k++++al++Gllllt+G +Gn+ir+l Plti+d+ +d
  lcl|FitnessBrowser__HerbieS:HSERO_RS05420 346 PQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMD 413
                                                ******************************************************************** PP

                                  TIGR00700 409 eglkileaal 418
                                                e+l il +a+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05420 414 EALGILAKAI 423
                                                ******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (426 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.66
//
[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