GapMind for catabolism of small carbon sources

 

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

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate 199928 SO0742 iron(III) ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::P31134
         (377 letters)



>FitnessBrowser__MR1:199928
          Length = 349

 Score =  215 bits (548), Expect = 1e-60
 Identities = 129/327 (39%), Positives = 192/327 (58%), Gaps = 18/327 (5%)

Query: 16  LTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQ 75
           +T  L +  +   Y GQ  +  + LT+ +GEI ALLG SGCGK+TLLR +AG +  S G+
Sbjct: 1   MTSTLNLHQVHSDYQGQQILKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGE 60

Query: 76  IMLDGVDLSQ----VPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVN 131
           I ++G  +S     VP   R I M+FQ YALFPH+TV +NI FG+   KL  A+  +R++
Sbjct: 61  IQINGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGVA--KLTTAQRKARLD 118

Query: 132 EMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLE 191
           +ML LV ++  AKR PH+LSGGQ+QRV++AR+LA  P+LLLLDEP   +D ++R  M  E
Sbjct: 119 DMLALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAE 178

Query: 192 VVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIG 251
           +  IL++  V+ V VTH ++EA   A  +AI ++G  VQ G  E++Y  P +RY A+F+G
Sbjct: 179 IRSILKQRNVSAVFVTHSKDEAFVFADTLAIFSQGVIVQHGRAEDLYAAPNSRYVADFLG 238

Query: 252 SVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPAN 311
           S N     L     DG  + +P  +  L+     S        V LRP+++ L  +    
Sbjct: 239 SGN----YLPAEVVDGHSVTTP--IGQLRSLTPLSQSHAFNGQVFLRPQQLALSAD---- 288

Query: 312 GCNFAVGEVIHIAYLGDLSVYHVRLKS 338
             +  VG +    +LG    Y V++++
Sbjct: 289 --DAGVGTITERRFLGAFCHYWVKVEA 313


Lambda     K      H
   0.321    0.137    0.400 

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: 302
Number of extensions: 11
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: 377
Length of database: 349
Length adjustment: 29
Effective length of query: 348
Effective length of database: 320
Effective search space:   111360
Effective search space used:   111360
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: 49 (23.5 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