GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frcA in Pseudomonas putida KT2440

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= uniprot:A0A0C4Y5F6
         (540 letters)



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

 Score =  320 bits (820), Expect = 8e-92
 Identities = 201/492 (40%), Positives = 286/492 (58%), Gaps = 33/492 (6%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPG---- 68
           +LA   + KT+     L +V L+  AGEV AL GENGAGKSTL K++SG      G    
Sbjct: 16  VLAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTY 74

Query: 69  -GECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDM 127
            G+ +  G R +      A  LGV ++ QEL+L P L+VAEN++L     R G ++   +
Sbjct: 75  RGQAYAPGSRGE------AERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRL 128

Query: 128 VRACAPTLARLGAD-FSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 186
            +     +AR+G D   P   V  L I  +Q+VEIAR +  +  +L++DEPT  L+  E 
Sbjct: 129 RQLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREV 188

Query: 187 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 246
             LF  I +LR  G+AI+YISHR+ E+  +A R+ VLRDG  V        S A LV +M
Sbjct: 189 ALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLM 248

Query: 247 VGRDLSGFYTKTHGQAVEREV---MLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGR 303
           VGR+L       H     R++   +L V  +  G +V+  SF++RAGE+ G++GL+GAGR
Sbjct: 249 VGRELG-----EHIDLGRRQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGR 303

Query: 304 TELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLD 363
           TEL RL++GAD    G + +  P  +  +       P+ A+ AGIA +TEDRK +GL L 
Sbjct: 304 TELLRLIYGADRADSGGIALGQPPQAVSI-----DSPKAAVRAGIALITEDRKGEGLLLT 358

Query: 364 QSVHENI---NLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQ 420
           QS+  NI   NL   +R     G L+  A +      I  + IR A AQ  VG LSGGNQ
Sbjct: 359 QSISANIALGNLGAVSR----AGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQ 414

Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480
           QKV++ R LE   +VL+ DEPTRG+D+GAK +IY L+  LA+ G A++++SS+L E++ +
Sbjct: 415 QKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLI 474

Query: 481 CDRVLVMREGTL 492
           CDR+ V+  G L
Sbjct: 475 CDRIAVLSAGRL 486



 Score = 90.9 bits (224), Expect = 1e-22
 Identities = 74/249 (29%), Positives = 121/249 (48%), Gaps = 13/249 (5%)

Query: 3   DMSDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGA 62
           D+      APLL +  +C+       +R+V     AGE+  + G  GAG++ L++++ GA
Sbjct: 258 DLGRRQLGAPLLKVDKLCRG----DKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGA 313

Query: 63  YTADPGG-ECHIDGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLGR--AL 116
             AD GG       Q V ID P++A   G+A+I ++     L    S++ NI LG   A+
Sbjct: 314 DRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAV 373

Query: 117 QRRGLVARGDMVRACAPTLARLGADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVM 174
            R G V   +  +A A    +     S  A   V  LS   +Q V I R +  + ++L+ 
Sbjct: 374 SRAG-VLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLF 432

Query: 175 DEPTTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDR 234
           DEPT  +       ++ L+ +L  +G A++ +S  + E+  + DR+ VL  G  + T  R
Sbjct: 433 DEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFAR 492

Query: 235 AHLSQAALV 243
            H SQ  L+
Sbjct: 493 DHWSQDQLL 501


Lambda     K      H
   0.320    0.136    0.382 

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: 664
Number of extensions: 46
Number of successful extensions: 10
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: 540
Length of database: 524
Length adjustment: 35
Effective length of query: 505
Effective length of database: 489
Effective search space:   246945
Effective search space used:   246945
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: 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 preprint 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