GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Halomonas xinjiangensis TRM 0175

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= reanno::Smeli:SMc02869
         (352 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  316 bits (809), Expect = 7e-91
 Identities = 166/307 (54%), Positives = 215/307 (70%), Gaps = 15/307 (4%)

Query: 17  VGSLQLKTIRKAF-GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGS 75
           + S+QL  ++K + G+ E +KGIDL++ DGEFV+ VGPSGCGKSTLLR +AGLE  T G+
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 76  VQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAG 135
           ++ID   V  + PA+R IAMVFQ+YALYPH+TV  N+  GLK  GV + EIE +V  AA 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 136 MLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARL 195
           ML +EP+L R+P +LSGGQRQRVA+GRA+VREP  FLFDEPLSNLDA LRV  R+EI +L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 196 HRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQM 255
            R LK T +YVTHDQ+EA+TL D++VVLN G IEQVG+PME+Y +PA++FVA FIGSP M
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 256 NFIEAAKLGD-----------GEAKTIGIRPEHIGLSRESGDW---KGKVIHVEHLGADT 301
           N +  A L +            +   IGIRP+ + +     D     G V   E  GA++
Sbjct: 241 NMLPVAYLRERGANGLLDHLAADTDVIGIRPDDLRIEAPDEDHLVVTGTVELFEAAGAES 300

Query: 302 IIYIESE 308
            +Y+  E
Sbjct: 301 HLYVSLE 307


Lambda     K      H
   0.320    0.137    0.393 

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: 351
Number of extensions: 14
Number of successful extensions: 1
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: 352
Length of database: 354
Length adjustment: 29
Effective length of query: 323
Effective length of database: 325
Effective search space:   104975
Effective search space used:   104975
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 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