Alignments for a candidate for TM1750 in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for TM1750 in Pseudomonas stutzeri RCH2

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF2021 Psest_2064 ABC-type uncharacterized transport system, duplicated ATPase component

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__psRCH2:GFF2021
          Length = 553

 Score =  243 bits (619), Expect = 1e-68
 Identities = 123/260 (47%), Positives = 183/260 (70%), Gaps = 8/260 (3%)

Query: 12  PLLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64
           PLL+  DL+ +FP  K +L       KAVDG++  + +G+TLG+VGESG GKSTLG  IL
Sbjct: 278 PLLEVDDLRVWFPIKKGLLRRTVDHIKAVDGVNFSLPKGQTLGIVGESGSGKSTLGLAIL 337

Query: 65  KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124
           +LL    G+I F+G+ + +++ ++++P R++MQ++FQDP GSL+P+M+VG+I+ + L IH
Sbjct: 338 RLLG-SRGEIRFQGQHLQSMSQRQVRPLRRQMQVVFQDPFGSLSPRMSVGQIVGEGLHIH 396

Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184
           ++G  KE+ + + E L  VG+  E  + +PHEFSGGQ+QRI IARAL L P  I+ DEP 
Sbjct: 397 RMGNAKEQEQAIIEALVEVGLDPETRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPT 456

Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244
           SALD ++Q Q+++LL  +Q K  ++YLFI+H+LAVV  +SH++ V+  G++VE G    I
Sbjct: 457 SALDRTVQRQVVELLRSLQAKYNLTYLFISHDLAVVRALSHQMMVVKQGQVVEQGAAADI 516

Query: 245 FLNPIHPYTRALLKSVPKIP 264
           F  P HPYT+ LL+S    P
Sbjct: 517 FAAPQHPYTQQLLESAFMAP 536



 Score =  206 bits (525), Expect = 8e-58
 Identities = 110/257 (42%), Positives = 171/257 (66%), Gaps = 8/257 (3%)

Query: 13  LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL----- 67
           L++  DL   F  G+++ + V+G++ +I++GETL LVGESG GKS    +IL+LL     
Sbjct: 10  LVEVRDLAVEFVTGEQVQRVVEGVTFDIRKGETLALVGESGSGKSVTAHSILRLLPYPLA 69

Query: 68  RPDGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126
           R   G+I F G+D+   ++K M+  R  ++ ++FQ+P+ SLNP  TVG+ I + L IHK 
Sbjct: 70  RHPQGQILFHGQDLLKADEKAMRKIRGNRIAMVFQEPMTSLNPLHTVGKQINEVLEIHKG 129

Query: 127 GTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184
              K    R  ELL++VGI   R+ I ++PHE SGGQ+QR+ IA ALA  P+ ++ DEP 
Sbjct: 130 LRGKAATARTLELLELVGIPEPRKRIRAYPHELSGGQRQRVVIAMALANEPELLIADEPT 189

Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244
           +ALDV++Q +I++LL+E+Q ++G++ L I+H+L +V  I+H+V VM  G++VE    + +
Sbjct: 190 TALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQRGRVVEQALCEDL 249

Query: 245 FLNPIHPYTRALLKSVP 261
           F  P HPYT+ LL + P
Sbjct: 250 FRAPQHPYTQELLAAEP 266


Lambda     K      H
   0.321    0.142    0.417 

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: 538
Number of extensions: 22
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 328
Length of database: 553
Length adjustment: 32
Effective length of query: 296
Effective length of database: 521
Effective search space:   154216
Effective search space used:   154216
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources