GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Sphingomonas koreensis DSMZ 15582

Align Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::Q97Q42
         (385 letters)



>FitnessBrowser__Korea:Ga0059261_1321
          Length = 238

 Score =  123 bits (308), Expect = 6e-33
 Identities = 81/219 (36%), Positives = 116/219 (52%), Gaps = 9/219 (4%)

Query: 4   PIIEFKNVSKVFEDSNT--KVLKDINFELEEGKFYTLLGASGSGKSTILNIIAGLLDATT 61
           PII  +N++KVF +  T  + LK ++ ++ E  F  ++G SGSGKST +NI+  L   T+
Sbjct: 6   PIIRLRNITKVFGEGATAFQALKGVDLDIAERDFVAVMGPSGSGKSTTMNILGCLDVPTS 65

Query: 62  GDIMLDGVRINDIPTNKRDVHT------VFQSYALFPHMNVFENVAFPLRLRKIDKKEIE 115
           G+ +  GV I  +  ++R +        VFQ + L    N  ENV  PL  R  DKK   
Sbjct: 66  GEFLFKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNALENVELPLLYRGEDKKVRH 125

Query: 116 QRVAEVLKMVQLEGYEKRSIRKLSGGQRQRVAIARAIINQPRVVLLDEPLSALDLKLRTD 175
           +     L+ V L  +   +  +LSGGQ QRVAIARAI+  P V+L DEP   LD     +
Sbjct: 126 ELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPAVLLADEPTGNLDSARSVE 185

Query: 176 MQYELRELQQRLGITFVFVTHDQEEALAMSDWIFVMNDG 214
           +   L  L +  GIT + VTH+ + A A +  I    DG
Sbjct: 186 IMELLTSLNKDSGITVLMVTHEPDMA-AFARTIVHFKDG 223


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: 190
Number of extensions: 5
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: 385
Length of database: 238
Length adjustment: 27
Effective length of query: 358
Effective length of database: 211
Effective search space:    75538
Effective search space used:    75538
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 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