GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Sinorhizobium meliloti 1021

Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate SMc00169 SMc00169 malic enzyme

Query= curated2:P39197
         (318 letters)



>FitnessBrowser__Smeli:SMc00169
          Length = 770

 Score =  155 bits (392), Expect = 3e-42
 Identities = 111/333 (33%), Positives = 161/333 (48%), Gaps = 25/333 (7%)

Query: 1   MKPLDRIHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEIPGAGR---- 56
           MKP+     A  A    +I  EGED RV  AA+ LL  G A+  L+G P+I         
Sbjct: 443 MKPV--FAAAKNAAKNRVIFAEGEDERVLRAAQVLLEEGTAKPILIGRPQIIETRLRRYG 500

Query: 57  -----------IDPAGGPDLAELADHWHRMRAARGMTAERALTEMRDPIRQ-AAMRVRLG 104
                      ++P G P   +  D +  +    G+  E A T +R       A+ V+ G
Sbjct: 501 LRIRPDVDFEVVNPEGDPRYRDYVDDYFALVGRLGVIPEAARTIVRTNTTVIGALAVKRG 560

Query: 105 QADGTVGGAVATTADTVRAALQIIGKAPGAGIVSSFFLMLSCGPGAPVRGGMIFADCGLV 164
           +AD  + G     +  +R   QIIGK  G    S+  L++S       RG   F D  + 
Sbjct: 561 EADALICGVEGRYSRHLRDVSQIIGKRSGVLDFSALSLLIS------QRGATFFTDTYVS 614

Query: 165 IQPDARELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIRAAAP 224
             P A E+A   + AA+  RR     PR AL+S S  GS +  S  ++R AL L+R  AP
Sbjct: 615 FSPSAEEIAQTTVMAANEIRRF-GITPRAALVSHSNFGSRDSESAFKMRTALQLVRELAP 673

Query: 225 GLEVDGEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLAGLTAIG 284
            LEVDGEM  D+A+ E +R R  P+S L G  N+ VFP+L   NI   + + +     +G
Sbjct: 674 DLEVDGEMHGDSAISEVLRQRVMPDSTLNGEANLLVFPNLDAANITLGVVKTMTDSLHVG 733

Query: 285 PILQGLAKPANDLSRACSVKDIVNATAITAMQT 317
           PIL G A PA+ LS + + + +VN  A+  +++
Sbjct: 734 PILLGSALPAHILSPSVTSRGVVNMAALAVVES 766


Lambda     K      H
   0.320    0.136    0.391 

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: 471
Number of extensions: 22
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: 318
Length of database: 770
Length adjustment: 34
Effective length of query: 284
Effective length of database: 736
Effective search space:   209024
Effective search space used:   209024
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: 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