GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Croceitalea dokdonensis DOKDO 023

Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate WP_054559671.1 I595_RS12000 ABC transporter ATP-binding protein

Query= TCDB::Q97Q42
         (385 letters)



>NCBI__GCF_001306415.1:WP_054559671.1
          Length = 234

 Score =  137 bits (344), Expect = 4e-37
 Identities = 87/225 (38%), Positives = 134/225 (59%), Gaps = 16/225 (7%)

Query: 5   IIEFKNVSKVFE--DSNTKVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATTG 62
           +IE K++ K ++   ++  VLK INF  E G+   ++G+SGSGKST+LNI+  L +A +G
Sbjct: 1   MIEIKDLHKSYKMGSNSLHVLKGINFSCEAGELVAIMGSSGSGKSTLLNILGMLDEADSG 60

Query: 63  DIMLDGVRINDIPTNKRDVHT------VFQSYALFPHMNVFENVAFPLRLRKIDKKEIEQ 116
              LDGV I ++   K   +       VFQS+ L  + +  ENVA PL  +K+ +KE ++
Sbjct: 61  SYTLDGVPIKNLSETKAAQYRNKFLGFVFQSFNLINYKSALENVALPLYYQKVARKERQE 120

Query: 117 RVAEVLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTDM 176
           +  + L+ V L+ +      +LSGGQ+QRVAIARA+  +P+V+L DEP  ALD K     
Sbjct: 121 KSLQYLERVGLKEWATHLPSELSGGQKQRVAIARAMAAEPKVLLADEPTGALDSK----T 176

Query: 177 QYELRELQQRL---GITFVFVTHDQEEALAMSDWIFVMNDGEIVQ 218
            YE+ +L Q++   G T + VTH+ + A  M   +  + DG IV+
Sbjct: 177 SYEVMDLIQKINDEGNTILVVTHEPDIA-EMCKRVIHLKDGVIVE 220


Lambda     K      H
   0.318    0.138    0.386 

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: 216
Number of extensions: 6
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: 385
Length of database: 234
Length adjustment: 27
Effective length of query: 358
Effective length of database: 207
Effective search space:    74106
Effective search space used:    74106
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: 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