GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas stutzeri RCH2

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family

Query= metacyc::MONOMER-11537
         (425 letters)



>FitnessBrowser__psRCH2:GFF2666
          Length = 406

 Score =  204 bits (520), Expect = 3e-57
 Identities = 145/415 (34%), Positives = 207/415 (49%), Gaps = 40/415 (9%)

Query: 23  IHPIFADSA------KNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTH 76
           I P FA +A        + V D  GRE +DFAGGIAV   GH HP ++AA+TEQ  KL H
Sbjct: 17  IVPTFAPAAFVPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWH 76

Query: 77  TCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATGRA 130
               +   EP + L +K+   V   FA +     +G+EA E A K+AR          + 
Sbjct: 77  IS-NIYTNEPALRLAKKL---VAATFADRAFFCNSGAEANEAAFKLARRYAHDVYGPQKF 132

Query: 131 GVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIER 190
            +I+   ++HGRT+ T+ + G+   YS G G    GI    Y N+L  +    S  +   
Sbjct: 133 EIISALNSFHGRTLFTVTVGGQS-KYSDGFGPKIEGITHVPY-NDLEALKAAISDKT--- 187

Query: 191 IFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTG 250
                       A+++EP+QGE G     + +++  R LC++H  LLI DEVQTG GRTG
Sbjct: 188 -----------CAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTG 236

Query: 251 TFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAAL 310
             FA    G+T D+ T AKS+ GGFP+  +    E    ++ G  G TY G+P+ACA A 
Sbjct: 237 ELFAYMHYGITPDILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAE 296

Query: 311 AVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPN 370
           AV+++     +L+  KA  ER    L  I  +Y V   VR  G +I   L    D+ K  
Sbjct: 297 AVVDIVNTPEVLEGVKAKHERFKARLTQIGERYGVFSLVRGRGLLIGCVL---SDAWKGK 353

Query: 371 AAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425
           A A     A A  + L++L  G   +V+R+   L    A +D+GL  +E   A L
Sbjct: 354 AGAFC---AAAEKEALMVLQAGP--DVVRLAPSLVIDQADIDEGLDRLERAVAAL 403


Lambda     K      H
   0.320    0.137    0.394 

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: 404
Number of extensions: 16
Number of successful extensions: 4
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: 425
Length of database: 406
Length adjustment: 31
Effective length of query: 394
Effective length of database: 375
Effective search space:   147750
Effective search space used:   147750
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 (21.8 bits)
S2: 50 (23.9 bits)

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