GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Shewanella oneidensis MR-1

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate 199928 SO0742 iron(III) ABC transporter, ATP-binding protein (NCBI ptt file)

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>FitnessBrowser__MR1:199928
          Length = 349

 Score =  150 bits (380), Expect = 3e-41
 Identities = 91/250 (36%), Positives = 143/250 (57%), Gaps = 22/250 (8%)

Query: 16  LEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILLD 75
           L +  +H  Y   ++LKG+DLT+ +G ++ L+G SG GKTTLLR V  L+    G+I   
Sbjct: 5   LNLHQVHSDYQGQQILKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEI--- 61

Query: 76  GESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLLKV----KK 131
                  ++NGK V  + + +   +   GM FQ + LFPHLT  +N+  G+ K+    +K
Sbjct: 62  -------QINGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGVAKLTTAQRK 114

Query: 132 LHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSAL 191
              D+ + L +  LE  GL +R   YP +LSGGQQQRV+IARA+A  P L+L DE  S +
Sbjct: 115 ARLDDMLALVK--LE--GLAKR---YPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNI 167

Query: 192 DPELVGEVLSVIKG-LAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELFER 250
           D ++   +++ I+  L +  ++ + VTH    AF  +D +   +QG I + G  ++L+  
Sbjct: 168 DAQVRHSMMAEIRSILKQRNVSAVFVTHSKDEAFVFADTLAIFSQGVIVQHGRAEDLYAA 227

Query: 251 PQSPRLAEFL 260
           P S  +A+FL
Sbjct: 228 PNSRYVADFL 237


Lambda     K      H
   0.319    0.135    0.379 

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: 220
Number of extensions: 10
Number of successful extensions: 4
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: 265
Length of database: 349
Length adjustment: 27
Effective length of query: 238
Effective length of database: 322
Effective search space:    76636
Effective search space used:    76636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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