GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sinorhizobium meliloti 1021

Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate SM_b20423 SM_b20423 hypothetical protein

Query= SwissProt::Q84P52
         (520 letters)



>FitnessBrowser__Smeli:SM_b20423
          Length = 458

 Score =  364 bits (934), Expect = e-105
 Identities = 183/433 (42%), Positives = 271/433 (62%), Gaps = 9/433 (2%)

Query: 76  GWHSTDLEPL-VIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATKQLNELA 134
           G H+    P  VI   EG Y+ D++GK+ LDA AGL+C ++G    ++  A  +Q   LA
Sbjct: 24  GMHARGETPTRVIGGGEGVYITDISGKRSLDAFAGLYCVNVGYGRQKIADAIAEQAKNLA 83

Query: 135 FYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNNALGRPD 194
           +YH++    T+ S+ L+K ++D      M++ +F  SGS+AN+T +KL+WYYNN LGRP+
Sbjct: 84  YYHAYVGHGTEASIRLSKMIIDR-APEGMSRVYFGLSGSDANETNIKLIWYYNNILGRPE 142

Query: 195 KKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGETEEEFS 254
           KKK I+R + YHGS +++ SL+GL   H  FDLP   +LHT+ P+++R      +EE+FS
Sbjct: 143 KKKIISRWRGYHGSGVMTGSLTGLHLFHNAFDLPRAPILHTEAPYYFRRPDRSMSEEQFS 202

Query: 255 TRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDILFIADEV 314
              A+ LE +IL EGP+T+AAFI EP++G GG++PPP  Y+EK+QA+L+KYDIL +ADEV
Sbjct: 203 QYCADKLEEMILAEGPDTVAAFIGEPILGTGGIVPPPKGYWEKIQAVLQKYDILLVADEV 262

Query: 315 ICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSNKLGTFS 374
           + GFGRLGTMFG + Y IKPDL+++AK L+S Y P+   +VS ++  V+   S++LG   
Sbjct: 263 VTGFGRLGTMFGSDHYGIKPDLITIAKGLTSAYAPLSGTIVSDKLWQVLVKGSDELGAIG 322

Query: 375 HGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGL-KAFSDSPIIGEIRGTGL 433
           HG+TYS HP+  A  +  L++  E  I+E        F+  L KA  D   +GE+RG GL
Sbjct: 323 HGWTYSAHPICAAAGIANLELIDELGIVENAGSTGAYFRAELQKAVGDHRHVGEVRGDGL 382

Query: 434 LHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRV--AGDNIMMSPPYILSLEEID 491
           +   EF +++     F P   +G    A   + GV+ R    GD +  +PP  L+ +E D
Sbjct: 383 MAAIEFVEDRDDRAFFDPGRKVGPQVAAALLERGVIGRAMPQGDILGFAPPLCLTRDEAD 442

Query: 492 ELIIKYGKALKDT 504
            ++    KA  DT
Sbjct: 443 IVV----KAAADT 451


Lambda     K      H
   0.317    0.135    0.401 

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: 628
Number of extensions: 21
Number of successful extensions: 3
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: 520
Length of database: 458
Length adjustment: 34
Effective length of query: 486
Effective length of database: 424
Effective search space:   206064
Effective search space used:   206064
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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