GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sinorhizobium fredii NGR234

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_015887459.1 NGR_RS06525 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_000018545.1:WP_015887459.1
          Length = 422

 Score =  546 bits (1406), Expect = e-160
 Identities = 268/416 (64%), Positives = 319/416 (76%)

Query: 8   LNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAI 67
           L  R+  A  RGVG+    YADRAENA +WD E   Y DFAAGIAV+NTGHRHP+V+ A+
Sbjct: 4   LTDRKNAAISRGVGMTTQIYADRAENAEIWDKESNRYIDFAAGIAVVNTGHRHPKVIAAV 63

Query: 68  AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127
            AQL+RFTHT +Q+VPY+ YV LAER+NAL P +   KT   TTGAEAVENA+KIARA T
Sbjct: 64  KAQLDRFTHTCHQVVPYENYVHLAERLNALAPGKFAKKTIFVTTGAEAVENAVKIARAAT 123

Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187
           GR  VIAF G FHGRT +GMALTGKV PYK+GFG  P+D++HAPFP  LHGVS E++L A
Sbjct: 124 GRQAVIAFGGGFHGRTFMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVSVEQSLAA 183

Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247
           L+ LF  D+DP RVAAII+EPVQGEGGF  AP  FM+ LR +CDQHGI+LIADEVQTGF 
Sbjct: 184 LKKLFAADVDPGRVAAIILEPVQGEGGFYPAPTAFMKALREICDQHGILLIADEVQTGFA 243

Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307
           RTGK+FAM HHDV PDL+TMAKSLAGG PL+AV+GRA IMDAP PGGLGGTY GNP+ +A
Sbjct: 244 RTGKLFAMEHHDVAPDLMTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPIGIA 303

Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQ 367
           AAHAV+DVIEEE+LCER+  LG +L++ L   R+  P + ++RG G M A EF D  T  
Sbjct: 304 AAHAVLDVIEEEQLCERANQLGNRLKQRLAQIREKAPEIVDIRGPGFMNAVEFNDVKTKL 363

Query: 368 PSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423
           PSAE A +V+  ALE GL+LLTCG +GNVIRFL P+TI    F  AL +L  ++ E
Sbjct: 364 PSAEFANKVRLIALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDILEASILE 419


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: 603
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: 422
Length adjustment: 32
Effective length of query: 391
Effective length of database: 390
Effective search space:   152490
Effective search space used:   152490
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 WP_015887459.1 NGR_RS06525 (4-aminobutyrate--2-oxoglutarate transaminase)
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.1389006.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-187  609.0   5.5   2.2e-187  608.7   5.5    1.0  1  NCBI__GCF_000018545.1:WP_015887459.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_015887459.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  608.7   5.5  2.2e-187  2.2e-187       2     418 ..       7     417 ..       6     419 .. 0.99

  Alignments for each domain:
  == domain 1  score: 608.7 bits;  conditional E-value: 2.2e-187
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           r++aa+s+Gvg+t++++a +ae+ae+ d + nr+id+aagiav+n+Gh+hPkv++avk q++++tht++qvvp
  NCBI__GCF_000018545.1:WP_015887459.1   7 RKNAAISRGVGMTTQIYADRAENAEIWDKESNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFTHTCHQVVP 79 
                                           7899********************************************************************* PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye yv+lae+lna+aPg   kk++++++Gaeavenavkiar+ tgr++v+af +gfhGrt++ malt+kv Py
  NCBI__GCF_000018545.1:WP_015887459.1  80 YENYVHLAERLNALAPGKFAKKTIFVTTGAEAVENAVKIARAATGRQAVIAFGGGFHGRTFMGMALTGKVVPY 152
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                           k+GfG ++++v++aP+p ++++ ++      ++ laa+++lf adv++ +vaa++lePvqGeGGf  ++  ++
  NCBI__GCF_000018545.1:WP_015887459.1 153 KVGFGAMPADVFHAPFPIELHGVSV------EQSLAALKKLFAADVDPGRVAAIILEPVQGEGGFYPAPTAFM 219
                                           *********************9988......45677************************************* PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                           +a++++c++hgi+liadevqtGfartGklfa+eh+d+ Pdl+t+aksla+G+Pl++v+Graei+dap pGglG
  NCBI__GCF_000018545.1:WP_015887459.1 220 KALREICDQHGILLIADEVQTGFARTGKLFAMEHHDVAPDLMTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLG 292
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePd 366
                                           Gty+GnP+++aaa+avld+ieee l+era+q+g+++k++l +++e+ p i d+rg G m ave++d +t+ P+
  NCBI__GCF_000018545.1:WP_015887459.1 293 GTYGGNPIGIAAAHAVLDVIEEEQLCERANQLGNRLKQRLAQIREKAPEIVDIRGPGFMNAVEFNDVKTKLPS 365
                                           ************************************************************************* PP

                             TIGR00700 367 aalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                           a  a+k+   al++Gl+llt+G++Gn+ir+l+P+ti de + e+l+ilea++
  NCBI__GCF_000018545.1:WP_015887459.1 366 AEFANKVRLIALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDILEASI 417
                                           ************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (422 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.26
//
[ok]

This GapMind analysis is from Apr 09 2024. 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