GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Pseudomonas simiae WCS417

Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__WCS417:GFF2673
          Length = 510

 Score =  412 bits (1059), Expect = e-119
 Identities = 230/498 (46%), Positives = 327/498 (65%), Gaps = 9/498 (1%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPD-AGEIR 81
           LLE+  ISK F G+  L  V L+V PG + ALMGENGAGKSTLMKI++G YQ D  GEIR
Sbjct: 6   LLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIR 65

Query: 82  LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141
           + G+ I    P  A+  GIA+I+QEL+L P++S+AENI++GRE L     ++ + M    
Sbjct: 66  IAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRE-LRRGWTIDRKGMEAGC 124

Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201
            E+L RL     P  +V +LSIAERQ+VEIA+A+   + IL+MDEPT+ ++ +E   LF+
Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184

Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261
           +I  L+SQG  I+YI+H+M E++A++D V+V RDGHYIG    D++++++L+ MMVGR+L
Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGRDL 244

Query: 262 SQLFPLRETPI--GDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319
           S  +         G++++ VRD+      +  SFDLHAGE+LGIAGL+G+GRT +A  IF
Sbjct: 245 SGFYKKEHAAYNPGNVVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTELARLIF 304

Query: 320 GITPSSSGQITLDGKAVR-ISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEM-AVLP 377
              P +SG + + GKAV  +  P  AI  G   LTEDRK  GLF  +SV +N+ + A +P
Sbjct: 305 AADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINVCACVP 364

Query: 378 HYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437
                G + +        D  K L ++  S +     LSGGNQQK LLAR L   P +LI
Sbjct: 365 DAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVKPHVLI 424

Query: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGEL---MG 494
           LDEPTRG+D+G+K+EIYR+I  LA  G+ +++ISSELPE++G  DRV++M EG+L   +G
Sbjct: 425 LDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQLVAEVG 484

Query: 495 TLDRSEATQEKVMQLASG 512
                  +QE+++ LA+G
Sbjct: 485 GASGQAISQERIIDLATG 502


Lambda     K      H
   0.320    0.136    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: 685
Number of extensions: 38
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: 517
Length of database: 510
Length adjustment: 35
Effective length of query: 482
Effective length of database: 475
Effective search space:   228950
Effective search space used:   228950
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