GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Halomonas xinjiangensis TRM 0175

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= reanno::Smeli:SM_b21216
         (360 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  293 bits (749), Expect = 6e-84
 Identities = 165/359 (45%), Positives = 230/359 (64%), Gaps = 16/359 (4%)

Query: 1   MSALEIRNIRKRY-GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59
           M+++++  ++K Y G VE +KGID+ +  GEF+VL+G SGCGKSTLL ++AGL   + G 
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  ILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTAR 119
           + I +R V  + P +RDIAMVFQ+YALYP+++V  N+ +GL+ R V + E ++ V D A 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 LLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRL 179
           +L+IE  L+RKP +LSGGQRQRVA+GRALVR P  FLFDEPLSNLDAKLR++MR E+K+L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 HQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPM 239
            + L+TT +YVTHDQ+EA+TL  R+ V+  G IEQ+  P EVY++PA+++VA F+GSP M
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 240 NILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQR-LTA 298
           N+L        L+  G   +L   AA            +GIRP+ LR+ A  E    +T 
Sbjct: 241 NMLPVAY----LRERGANGLLDHLAADTDV--------IGIRPDDLRIEAPDEDHLVVTG 288

Query: 299 SVEVVELTGPE--LVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGR 355
           +VE+ E  G E  L  +     Q        R  V  G    F    +ALH F+  SG+
Sbjct: 289 TVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRFHVLPSALHPFNQASGK 347


Lambda     K      H
   0.320    0.136    0.385 

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: 361
Number of extensions: 15
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: 360
Length of database: 354
Length adjustment: 29
Effective length of query: 331
Effective length of database: 325
Effective search space:   107575
Effective search space used:   107575
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