Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N2E2

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  377 bits (967), Expect = e-109
 Identities = 210/476 (44%), Positives = 308/476 (64%), Gaps = 22/476 (4%)

Query: 45  LIGENGAGKSTLIKILTGVLKPDAGE--ILVNGERVEFH-SPVDAFKKGISVIHQELNLC 101
           L+GENGAGKST++KIL G    DAG+  +  NG  +  H +P+   + GI  I+QE NL 
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60

Query: 102 DNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQ 161
            +M+VAEN++L  E +R         VD   M++ ++ +LD +G   +P  +VR L+ A+
Sbjct: 61  ADMSVAENMYLGREPLR------HGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAE 114

Query: 162 RQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMR 221
           +QMVEI KAL    ++I MDEPT++L+  E ++L EII  LK++GIS+++VSH+L+EV  
Sbjct: 115 QQMVEIAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKA 174

Query: 222 ISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREVEFFPHGIETRPGEIALEVRNLK-- 279
             DR  + RDG  I      +  VD I+++MVGR+VEF    +   PGE+ L+V+++   
Sbjct: 175 CCDRYTIFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRT 234

Query: 280 --------WKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRK 331
                       + ++S +VR GE++GFAGLVGAGRTE   ++FG +  + G IYVNGR+
Sbjct: 235 AAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQ 294

Query: 332 VE-IKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEI 390
           V   K+P + I  G+ L+PEDRK Q   L  +++ N+ LPSL  + RWG+ +D+R E ++
Sbjct: 295 VSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQL 354

Query: 391 SEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEI 450
            +DY KRL IK  +       LSGGNQQKV+LA+ +A    +LI DEPTRGIDVGAKAE+
Sbjct: 355 IQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEV 414

Query: 451 HRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLDNREKRVTQEEIM 506
           H+++ ++A  G AVI+ISSELPE++ +SDRIV   EG+IT ++   E   T+E +M
Sbjct: 415 HQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADE--ATEELLM 468



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 60/247 (24%), Positives = 117/247 (47%), Gaps = 25/247 (10%)

Query: 32  NVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVE-FHSPVDAFKKG 90
           ++  +V   EIV   G  GAG++ L +++ G    D G I VNG +V  F SP +    G
Sbjct: 249 DMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPFKSPREGIAAG 308

Query: 91  ISVIHQELNLCDNMTVAENIFLAYE--------AVRGQKRT---LSSRVDENYMYTRSKE 139
           ++++ ++          +  FL++         ++ G +R    +  R +   +    K 
Sbjct: 309 VALVPEDRK-------QQACFLSHSIRWNMSLPSLGGLQRWGMFIDDRAETQLIQDYQKR 361

Query: 140 LLDLIGAKFSPDAL-VRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEI 198
           L      K S D++ +  L+   +Q V + + +  +P+++ +DEPT  + V     + ++
Sbjct: 362 LR----IKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQL 417

Query: 199 IEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII-KMMVGREV 257
           +  +   G++V+ +S  L EVM +SDRIV  R+G+  G +   E   + ++ +M  G   
Sbjct: 418 LFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLMARMAQGVSS 477

Query: 258 EFFPHGI 264
            F   G+
Sbjct: 478 SFSQQGV 484


Lambda     K      H
   0.319    0.138    0.381 

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: 620
Number of extensions: 31
Number of successful extensions: 8
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: 520
Length of database: 485
Length adjustment: 34
Effective length of query: 486
Effective length of database: 451
Effective search space:   219186
Effective search space used:   219186
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 (21.7 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:

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