GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Sinorhizobium meliloti 1021

Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate SMc00078 SMc00078 Leu/Ile/Val-binding protein

Query= uniprot:Q1MDE9
         (367 letters)



>FitnessBrowser__Smeli:SMc00078
          Length = 368

 Score =  540 bits (1391), Expect = e-158
 Identities = 266/368 (72%), Positives = 312/368 (84%), Gaps = 1/368 (0%)

Query: 1   MTLKTLTA-TLVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGG 59
           M L  LT   L AS+AFAPLAHADITIG+I PLTGPVAA+G+QVKNGA+ AV+ IN  GG
Sbjct: 1   MRLSRLTGMALAASVAFAPLAHADITIGVITPLTGPVAAFGEQVKNGAEAAVEAINSAGG 60

Query: 60  ILGEKVVLELADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVT 119
           + GEK+V+++ DDAGEPKQ VS AN++ G+GI++VVGPV SG ++P SDVLAENG+LMVT
Sbjct: 61  VNGEKLVVKIVDDAGEPKQAVSVANQLAGEGIQYVVGPVLSGTSMPASDVLAENGILMVT 120

Query: 120 PTATAPDLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAF 179
           PTAT PDLT RGL NVLRTCGRDDQQA VAA YV+KNFKDKRVA+++DKGAYGKGLAD F
Sbjct: 121 PTATTPDLTTRGLWNVLRTCGRDDQQAVVAADYVVKNFKDKRVAVLHDKGAYGKGLADGF 180

Query: 180 KATLNAGGITEVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAA 239
           KA +NAGGITEVV + +TPG+KDF A+ TR+K+E VDVVYFGGYH EGGLLARQ+HD   
Sbjct: 181 KAAINAGGITEVVYEGLTPGEKDFGAIVTRLKAENVDVVYFGGYHAEGGLLARQMHDQGV 240

Query: 240 NATIIGGDGLSNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAAKNIPAEAFTLN 299
            A ++GGDGLSNTEFWAIG +AA GT++TNASDAT++P +    +AL AKNIPAEAFTLN
Sbjct: 241 KAQLLGGDGLSNTEFWAIGGEAASGTVYTNASDATRNPAAAPVIEALKAKNIPAEAFTLN 300

Query: 300 AYAAVEVLKAGIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWE 359
           AYAAV+VLKAGIEKAGS EDA AVATA+K G+ I T IGK+TYGE+GDLTS SFSLYKWE
Sbjct: 301 AYAAVQVLKAGIEKAGSTEDATAVATAIKSGEAIDTVIGKLTYGESGDLTSPSFSLYKWE 360

Query: 360 AGKIVAAE 367
            G+ VA E
Sbjct: 361 GGQSVAVE 368


Lambda     K      H
   0.312    0.131    0.362 

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: 535
Number of extensions: 14
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: 367
Length of database: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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