Alignments for a candidate for gabT in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Sinorhizobium meliloti 1021

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate SM_b21186 SM_b21186 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__Smeli:SM_b21186
          Length = 422

 Score =  544 bits (1401), Expect = e-159
 Identities = 267/416 (64%), Positives = 316/416 (75%)

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

Query: 68  AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127
            AQL+RFTHT +Q+VPY+ YV LAER+NA+VP     KT   TTGAEAVENA+KIARA T
Sbjct: 64  KAQLDRFTHTCHQVVPYENYVHLAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIARAAT 123

Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187
           GR  V+AF G FHGRT +GMALTGKV PYK+GFG  P+D++HAPFP  LHGV+ E++L A
Sbjct: 124 GRQAVVAFGGGFHGRTFMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVTVEQSLSA 183

Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247
           L+ LF  D+DPARVAAII+EPVQGEGGF   P  FM+ LR VCDQHGI+LIADEVQTGF 
Sbjct: 184 LKKLFAADVDPARVAAIIIEPVQGEGGFYPVPTAFMKALREVCDQHGILLIADEVQTGFA 243

Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307
           RTGK+FAM HH V PDL TMAKSLAGG PL+AV+GRA IMDAP PGGLGGTY GNPL +A
Sbjct: 244 RTGKLFAMEHHGVAPDLTTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPLGIA 303

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

Query: 368 PSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423
           PSAE A +V+  ALE GL+LLTCG +GNVIRFL P+TI    F  AL  +  ++ E
Sbjct: 364 PSAEFANKVRLLALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDTIEASILE 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: 17
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 SM_b21186 SM_b21186 (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.14167.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   3.2e-184  598.3   6.6   3.9e-184  598.0   6.6    1.0  1  lcl|FitnessBrowser__Smeli:SM_b21186  SM_b21186 4-aminobutyrate aminot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SM_b21186  SM_b21186 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.0   6.6  3.9e-184  3.9e-184       2     418 ..       7     417 ..       6     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 598.0 bits;  conditional E-value: 3.9e-184
                            TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpy 75 
                                          r++aa+s+Gvg+t++v+a +ae+ae+ d +Gnr+id+aagiav+n+Gh+hPkv++avk q++++tht++qvvpy
  lcl|FitnessBrowser__Smeli:SM_b21186   7 RKNAAISRGVGMTTQVYADRAENAEIWDKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFTHTCHQVVPY 80 
                                          7899********************************************************************** PP

                            TIGR00700  76 esyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPyki 149
                                          e yv+lae+lnai Pg   kk++++++Gaeavenavkiar+ tgr++vvaf +gfhGrt++ malt+kv Pyk+
  lcl|FitnessBrowser__Smeli:SM_b21186  81 ENYVHLAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIARAATGRQAVVAFGGGFHGRTFMGMALTGKVVPYKV 154
                                          ************************************************************************** PP

                            TIGR00700 150 GfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaav 223
                                          GfG ++++v++aP+p ++++ ++  ++s    l+a+++lf adv++ +vaa+++ePvqGeGGf   +  +++a+
  lcl|FitnessBrowser__Smeli:SM_b21186 155 GFGAMPADVFHAPFPIELHGVTV--EQS----LSALKKLFAADVDPARVAAIIIEPVQGEGGFYPVPTAFMKAL 222
                                          *******************9988..445....55**************************************** PP

                            TIGR00700 224 aslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtya 297
                                          +++c++hgi+liadevqtGfartGklfa+eh+++ Pdl t+aksla+G+Pl++v+Graei+dap pGglGGty+
  lcl|FitnessBrowser__Smeli:SM_b21186 223 REVCDQHGILLIADEVQTGFARTGKLFAMEHHGVAPDLTTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYG 296
                                          ************************************************************************** PP

                            TIGR00700 298 GnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePdaalae 371
                                          GnPl++aaa+avld+i ee l+era+q+g+++k++l  ++e+ p i d+rg G m ave++d  t+ P+a  a+
  lcl|FitnessBrowser__Smeli:SM_b21186 297 GNPLGIAAAHAVLDVIAEENLCERANQLGNRLKQRLAAIREKAPEIVDIRGPGFMNAVEFNDVRTNLPSAEFAN 370
                                          ************************************************************************** PP

                            TIGR00700 372 kiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                          k+   al++Gl+llt+G++Gn+ir+l+P+ti de + e+l+ +ea++
  lcl|FitnessBrowser__Smeli:SM_b21186 371 KVRLLALEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDTIEASI 417
                                          *****************************************999865 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.17
//
[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