GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Shewanella sp. ANA-3

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 7023651 Shewana3_0880 ABC transporter related (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_03040
         (254 letters)



>FitnessBrowser__ANA3:7023651
          Length = 241

 Score =  251 bits (641), Expect = 1e-71
 Identities = 130/251 (51%), Positives = 177/251 (70%), Gaps = 11/251 (4%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           + + +LHK YG + VLKG++     G+V+S+IG SGSGKSTFLRCINLLE+P  G I + 
Sbjct: 2   INITNLHKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLEKPTQGDIEIE 61

Query: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123
            +    +  KD  +         ++R ++ MVFQ+FNL+ H T ++NI  APV +  M++
Sbjct: 62  GQS---ITAKDACV--------DKLRQKVGMVFQNFNLFPHKTVLQNITLAPVSLKLMTQ 110

Query: 124 AEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183
           AEA  KA   L +VG+  + +AYP  +SGG++QRVAIARALAMEP++MLFDEPTSALDPE
Sbjct: 111 AEADNKALALLTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPE 170

Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243
           +VGDVL VM+ LAQ+G TMV+VTHEMGFAR+VS++++F+  G V ES  P E+   P+  
Sbjct: 171 MVGDVLDVMKDLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKEA 230

Query: 244 RLQQFLSGSLK 254
           R Q FLS  L+
Sbjct: 231 RTQSFLSKVLR 241


Lambda     K      H
   0.317    0.131    0.364 

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: 193
Number of extensions: 4
Number of successful extensions: 2
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: 254
Length of database: 241
Length adjustment: 24
Effective length of query: 230
Effective length of database: 217
Effective search space:    49910
Effective search space used:    49910
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 (21.7 bits)
S2: 46 (22.3 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