GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Caldicellulosiruptor hydrothermalis 108

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_013403235.1 CALHY_RS06825 branched-chain amino acid ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>NCBI__GCF_000166355.1:WP_013403235.1
          Length = 294

 Score =  153 bits (386), Expect = 5e-42
 Identities = 94/284 (33%), Positives = 164/284 (57%), Gaps = 11/284 (3%)

Query: 5   QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTS-GINLWLSM 63
           Q + NGI +GS+ AL ++G T+ YGI++L NFAHGD   + AY+ + + T   + L  S+
Sbjct: 6   QQLINGITLGSVYALISLGYTMVYGIIKLINFAHGDIFMVGAYIAYLSVTYLKLGLIPSL 65

Query: 64  ALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGNNQNYRV 123
            +  V   I   + E   +KP+R   +   + +I +IG++L L N + +I G +++ +  
Sbjct: 66  IVSMVFCSILGMLIEKFAYKPLR--NSPRISALITAIGVSLLLENLMQIIMGADSRVFPR 123

Query: 124 PIVPA-----QDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLAK 178
            +        QD + +  +   LL+I + +  M++L+ ++++TK+GKAMRAV+ ++D A+
Sbjct: 124 LVAEKNYHLFQDRIVVNNKQIYLLIITVLL--MIILNFVVKKTKIGKAMRAVSQDMDAAR 181

Query: 179 VSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVILGGIGNPY 237
           + GINV+  + +T+ + + L A  G + GL   T+ P MG    L  F + + GGIG   
Sbjct: 182 LMGINVDTTISYTFAIGSALAAAAGVLVGLYYNTINPLMGVLPGLKAFIAAVFGGIGIIP 241

Query: 238 GAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281
           GA+ GG  +G+ + +   +  + YK  VA  L+I+IL I+P GL
Sbjct: 242 GAMLGGFSLGIIETLVSGYGSSMYKDAVAFALLILILIIKPSGL 285


Lambda     K      H
   0.329    0.143    0.450 

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: 201
Number of extensions: 13
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: 286
Length of database: 294
Length adjustment: 26
Effective length of query: 260
Effective length of database: 268
Effective search space:    69680
Effective search space used:    69680
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