GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF2673 PS417_13635 D-ribose transporter
           ATP-binding protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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