GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_2455
          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:

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