Alignments for a candidate for gabT in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Paraburkholderia bryophila 376MFSha3.1

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Burk376:H281DRAFT_03179
          Length = 429

 Score =  601 bits (1549), Expect = e-176
 Identities = 293/423 (69%), Positives = 343/423 (81%)

Query: 1   MTMKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRH 60
           M +KN EL  R+  ATPRGVGVMCDFYA+RA+NA LWDVEGR + DFAAGIAV NTGHRH
Sbjct: 1   MNLKNAELKSRKDAATPRGVGVMCDFYAERAQNAELWDVEGRRFIDFAAGIAVCNTGHRH 60

Query: 61  PRVMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAI 120
           P+++ AI  QL+RFTHTAYQIVPY  YV LAE++N   P     KTA FTTGAEAVENAI
Sbjct: 61  PKIVAAIRDQLDRFTHTAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAI 120

Query: 121 KIARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVS 180
           KIARA TGRPGVIAF+G FHGRTL+GMALTGKVAPYK GFGPFPSD++HAPFP+ LHGVS
Sbjct: 121 KIARAATGRPGVIAFTGGFHGRTLMGMALTGKVAPYKAGFGPFPSDVFHAPFPNPLHGVS 180

Query: 181 TERALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIAD 240
           T  +L+A+E LFK DIDP RVAAII EPVQGEGGF  APA+F+R LR +C++HGI+LIAD
Sbjct: 181 TADSLKAIEFLFKADIDPKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIAD 240

Query: 241 EVQTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYA 300
           EVQTGF RTGK+FAM H+DV PDL+T+AKSLAGGMPLS V GRA +MDA  PGGLGGTYA
Sbjct: 241 EVQTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYA 300

Query: 301 GNPLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEF 360
           GNPLAVAAA AV+D+I+EEKLCER+  LG +++  L+A +   P +A+VRG G MVA EF
Sbjct: 301 GNPLAVAAALAVLDIIDEEKLCERATILGDRVKAKLIALQNEAPQIADVRGPGGMVAVEF 360

Query: 361 CDPATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQA 420
           C P + +P AE  KRVQTRAL+ GL+LL CG Y NV+RFL+PLTI    FD ALA+L   
Sbjct: 361 CKPGSTEPDAEFTKRVQTRALKRGLLLLVCGVYSNVVRFLFPLTIEDTVFDEALAILEDV 420

Query: 421 LAE 423
           + +
Sbjct: 421 IKD 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: 645
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: 429
Length adjustment: 32
Effective length of query: 391
Effective length of database: 397
Effective search space:   155227
Effective search space used:   155227
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 H281DRAFT_03179 H281DRAFT_03179 (4-aminobutyrate aminotransferase apoenzyme)
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.16314.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.2e-200  650.3   0.7   6.1e-200  650.1   0.7    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_03179  H281DRAFT_03179 4-aminobutyrate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03179  H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  650.1   0.7  6.1e-200  6.1e-200       2     420 .]      11     423 ..      10     423 .. 0.99

  Alignments for each domain:
  == domain 1  score: 650.1 bits;  conditional E-value: 6.1e-200
                                    TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelth 67 
                                                  r++aa+++Gvgv+++++a +a++ael dv+G+r+id+aagiav n+Gh+hPk+v+a++ q++++th
  lcl|FitnessBrowser__Burk376:H281DRAFT_03179  11 RKDAATPRGVGVMCDFYAERAQNAELWDVEGRRFIDFAAGIAVCNTGHRHPKIVAAIRDQLDRFTH 76 
                                                  899*************************************************************** PP

                                    TIGR00700  68 tafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGr 133
                                                  ta+q+vpy syvelaekln+ aPg ++kk++++++Gaeavena+kiar+ tgrpgv+af++gfhGr
  lcl|FitnessBrowser__Burk376:H281DRAFT_03179  77 TAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGR 142
                                                  ****************************************************************** PP

                                    TIGR00700 134 tnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqva 199
                                                  t + malt+kv+Pyk GfGPf+++v++aP+p ++++ ++       d l+aie lf+ad+++++va
  lcl|FitnessBrowser__Burk376:H281DRAFT_03179 143 TLMGMALTGKVAPYKAGFGPFPSDVFHAPFPNPLHGVST------ADSLKAIEFLFKADIDPKRVA 202
                                                  ************************************999......34677**************** PP

                                    TIGR00700 200 avvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitva 265
                                                  a+++ePvqGeGGf  ++ e+v a+++lc+ehgi+liadevqtGfartGklfa++h+d++Pdl+tva
  lcl|FitnessBrowser__Burk376:H281DRAFT_03179 203 AIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHHYDVVPDLMTVA 268
                                                  ****************************************************************** PP

                                    TIGR00700 266 ksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkd 331
                                                  ksla+G+Plsgv+Gra+++da+apGglGGtyaGnPlavaaalavldii+ee l+era  +g +vk 
  lcl|FitnessBrowser__Burk376:H281DRAFT_03179 269 KSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAALAVLDIIDEEKLCERATILGDRVKA 334
                                                  ****************************************************************** PP

                                    TIGR00700 332 klielkeevpaigdvrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirll 397
                                                  kli l++e p+i+dvrg G m+ave+ +p++tePda  +++++++al++Gllll +G++ n++r+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_03179 335 KLIALQNEAPQIADVRGPGGMVAVEFCKPGSTEPDAEFTKRVQTRALKRGLLLLVCGVYSNVVRFL 400
                                                  ****************************************************************** PP

                                    TIGR00700 398 tPltisdelldeglkileaalad 420
                                                   Plti d+ +de+l ile++++d
  lcl|FitnessBrowser__Burk376:H281DRAFT_03179 401 FPLTIEDTVFDEALAILEDVIKD 423
                                                  *******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (429 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: 00:00:00.02
# Mc/sec: 7.69
//
[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