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.2109886.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.99
//
[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:

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:

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:

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:

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