GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS34245 in Pseudomonas putida KT2440

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= uniprot:B2T9V9
         (510 letters)



>lcl|FitnessBrowser__Putida:PP_2455 PP_2455 ribose ABC transporter -
           ATP-binding subunit
          Length = 524

 Score =  253 bits (647), Expect = 9e-72
 Identities = 171/506 (33%), Positives = 266/506 (52%), Gaps = 22/506 (4%)

Query: 10  SSVPVV--EALEVTKRFGSTAA---LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLR 64
           S++P +  E +      G T A   L +VS+ +  GE  AL G NGAGKSTL  +++GL 
Sbjct: 6   SAMPALANEVVLAASGLGKTYAQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLE 65

Query: 65  KPDTGEVRFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDW 124
            P TG + + G A    +  +A R  V  V Q   ++  L+VAENLF++  P R G I  
Sbjct: 66  VPTTGHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISH 125

Query: 125 QAMRRDARALLDHWKID-VREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDG 183
           + +R+ A A +    +D +  D   G+L +  +Q+VEIAR L      +ILDEPTA L  
Sbjct: 126 KRLRQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTA 185

Query: 184 DEIKRLFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLI 243
            E+  LF +I  L+  GV  ++ISH L+E+  + Q + VLRD + +   P+      +L+
Sbjct: 186 REVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELV 245

Query: 244 EAMTGERGGLAVADAAARGALPADTAVALELKELTGAD-YEGVSFTVKRGEVVGLTGATS 302
             M G   G  +     +   P      L++ +L   D    VSF V+ GE+ G++G   
Sbjct: 246 NLMVGRELGEHIDLGRRQLGAPL-----LKVDKLCRGDKVREVSFEVRAGEIFGISGLIG 300

Query: 303 SGRTSVAEAIAGLRAAKRGTISVDGAILPPGDVP-----ASLAHGIGCVPKDRHHEGLVL 357
           +GRT +   I G   A  G I++     PP  V      A++  GI  + +DR  EGL+L
Sbjct: 301 AGRTELLRLIYGADRADSGGIALGQ---PPQAVSIDSPKAAVRAGIALITEDRKGEGLLL 357

Query: 358 TQSVAENASMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKV 417
           TQS++ N ++     + + G+     + A  ++ I A+ I + G + VV  LSGGNQQKV
Sbjct: 358 TQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKV 417

Query: 418 VMARALATNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDLR-TCDR 476
           V+ R L  +  VL+  +PT G+DV +K  +  ++  +  +GKA++VVS +L +L   CDR
Sbjct: 418 VIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDR 477

Query: 477 VLVMFRGRVAAEFPAG-WQDHDLIAS 501
           + V+  GR+   F    W    L+A+
Sbjct: 478 IAVLSAGRLIDTFARDHWSQDQLLAA 503


Lambda     K      H
   0.318    0.134    0.377 

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: 581
Number of extensions: 28
Number of successful extensions: 9
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: 510
Length of database: 524
Length adjustment: 35
Effective length of query: 475
Effective length of database: 489
Effective search space:   232275
Effective search space used:   232275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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