Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N1B4

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410
          Length = 514

 Score =  347 bits (890), Expect = e-100
 Identities = 194/485 (40%), Positives = 296/485 (61%), Gaps = 9/485 (1%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           L+  GI K FPGV A+D + F  +  ++ +L+GENGAGKSTL+KIL G   P +G++ + 
Sbjct: 16  LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
            ++  F S  D+   G++VIHQEL+L   MTVAEN+FL      G        ++   + 
Sbjct: 76  EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFL------GHLPASFGLINRGVLR 129

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
            ++   L  +  +  P   V  L+  QRQ+VEI KAL +   +I  DEPTSSL+  E +R
Sbjct: 130 QQALACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDR 189

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKK-GEFDVDTIIKMMV 253
           L  II  L+  G  V++VSHR++EV RI + + V +DG+ +   +       D ++  MV
Sbjct: 190 LMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMV 249

Query: 254 GREVEFFPHGIETRP-GEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312
           GR+++   +   +RP G +AL+V  L      + VSFE  KGE+LG  GLVGAGRTE   
Sbjct: 250 GRDIQDI-YDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFR 308

Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372
           ++ G+ +  +G + + GR++++ +P DAI  GI L PEDRK +G++   +V +NI + + 
Sbjct: 309 MLSGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISAR 368

Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432
              S +G +L    E++ ++  +K L +KTP+  Q    LSGGNQQK +L +WL+    +
Sbjct: 369 GAHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKV 428

Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492
           L+ DEPTRGID+GAKAEI+++I  LAA G AVI++SS+L E++ +SDRI+V+ EG +   
Sbjct: 429 LLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGE 488

Query: 493 LDNRE 497
           L   +
Sbjct: 489 LTREQ 493



 Score = 96.3 bits (238), Expect = 2e-24
 Identities = 64/229 (27%), Positives = 122/229 (53%), Gaps = 9/229 (3%)

Query: 33  VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92
           V FE ++ EI+ L G  GAG++ L ++L+G+ +  AG + + G  ++ HSP DA   GI 
Sbjct: 283 VSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPRDAIAAGIL 342

Query: 93  VIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149
           +  ++     +    +VAENI ++    RG   T    +   +    + + +  +  K +
Sbjct: 343 LCPEDRKKEGILPLASVAENINIS---ARGAHSTFGCLLRGLWEKDNADKQIKALKVK-T 398

Query: 150 PDAL--VRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGI 207
           P+A   +  L+   +Q   + + L    +++ +DEPT  + +     +++II  L + GI
Sbjct: 399 PNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAASGI 458

Query: 208 SVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGRE 256
           +V+ VS  L EVM ISDRI+V+ +G   GEL + + +   ++++ + R+
Sbjct: 459 AVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQ 507


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: 661
Number of extensions: 36
Number of successful extensions: 7
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: 514
Length adjustment: 35
Effective length of query: 485
Effective length of database: 479
Effective search space:   232315
Effective search space used:   232315
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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