GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components

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



>FitnessBrowser__psRCH2:GFF1860
          Length = 390

 Score =  351 bits (900), Expect = e-101
 Identities = 191/368 (51%), Positives = 249/368 (67%), Gaps = 14/368 (3%)

Query: 1   MSALEIRNIRKRYG--EVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58
           M++LE+RN++K YG  ++ TLK I + +++GEFL+L+G SGCGKSTL+N IAGL   +GG
Sbjct: 1   MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60

Query: 59  DILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTA 118
           +IL+    +    PKDRDIAMVFQSYALYP +SV  NI FGL+MR+VP A+ ++ V   A
Sbjct: 61  EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120

Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178
           +LLQIE LL+RKPSQLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K 
Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180

Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238
           +HQ L+TT VYVTHDQIEAMTL  ++AVM+DG I+Q   P E+Y+ PA L+VA F+GSPP
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240

Query: 239 MNILDAEMTANGLKIEG--------CEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLA-A 289
           MN +   +     +  G        CE  LPLP   +      R + +GIRPE + LA A
Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCE--LPLPITSDDGL-RDRELILGIRPEQIGLAPA 297

Query: 290 GSEAQRLTASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLF 349
           GS    L   +EVVE TGP+ +   T+   +    L P  A  +G      FD     LF
Sbjct: 298 GSADFSLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNLQFDPRRALLF 357

Query: 350 DPESGRSL 357
           D ++G  L
Sbjct: 358 DAQTGERL 365


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: 425
Number of extensions: 21
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: 360
Length of database: 390
Length adjustment: 30
Effective length of query: 330
Effective length of database: 360
Effective search space:   118800
Effective search space used:   118800
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: 50 (23.9 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