GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Caldicellulosiruptor hydrothermalis 108

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate WP_013403235.1 CALHY_RS06825 branched-chain amino acid ABC transporter permease

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>NCBI__GCF_000166355.1:WP_013403235.1
          Length = 294

 Score =  276 bits (706), Expect = 4e-79
 Identities = 141/302 (46%), Positives = 208/302 (68%), Gaps = 9/302 (2%)

Query: 1   MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSL 60
           M  F+QQLING++LG++Y LI++GYTMVYGII +INFAHG+I+M+GA++A         L
Sbjct: 1   MSTFIQQLINGITLGSVYALISLGYTMVYGIIKLINFAHGDIFMVGAYIAY--------L 52

Query: 61  GITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQI 120
            +T++ L L+  L+ SM+F ++ G  +E+ AY+PLR+SPR++ LI+AIG+S+ L+N +QI
Sbjct: 53  SVTYLKLGLIPSLIVSMVFCSILGMLIEKFAYKPLRNSPRISALITAIGVSLLLENLMQI 112

Query: 121 LQGARSKPLQPILPG-NLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179
           + GA S+    ++   N  L    + V+  ++  ++IT+ LM     ++ +T +G+A RA
Sbjct: 113 IMGADSRVFPRLVAEKNYHLFQDRIVVNNKQIYLLIITVLLMIILNFVVKKTKIGKAMRA 172

Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239
             QD   A L+G+NVD  IS TF +G+ALAA AG++V L Y  I+  +G L G+KAF AA
Sbjct: 173 VSQDMDAARLMGINVDTTISYTFAIGSALAAAAGVLVGLYYNTINPLMGVLPGLKAFIAA 232

Query: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIE 299
           V GGIG +PGAMLGG  +G+IE   SGY  S +KD   F +L+L+LI +P+GLLG+   E
Sbjct: 233 VFGGIGIIPGAMLGGFSLGIIETLVSGYGSSMYKDAVAFALLILILIIKPSGLLGKNIKE 292

Query: 300 KV 301
           KV
Sbjct: 293 KV 294


Lambda     K      H
   0.329    0.144    0.425 

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: 337
Number of extensions: 20
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: 301
Length of database: 294
Length adjustment: 26
Effective length of query: 275
Effective length of database: 268
Effective search space:    73700
Effective search space used:    73700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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