GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_2455
          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:

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