Alignments for a candidate for cbp in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for cbp in Pseudomonas stutzeri RCH2

Align cellobiose phosphorylase (EC 2.4.1.20) (characterized)
to candidate GFF2709 Psest_2763 Cellobiose phosphorylase

Query= BRENDA::Q9X2G3
         (813 letters)



>FitnessBrowser__psRCH2:GFF2709
          Length = 2843

 Score =  332 bits (850), Expect = 2e-94
 Identities = 255/841 (30%), Positives = 394/841 (46%), Gaps = 84/841 (9%)

Query: 4    GYFDDVNREYVITTP---QTPYPWINYLGTEDFFSIISHMAGGYCFYKDARLRRITRFRY 60
            G FD   REYV        TP PWIN +    F   +S    GY + +++R  ++T +  
Sbjct: 2047 GGFDKDGREYVTLLDAGANTPAPWINVIANPQFGFQVSAQGSGYTWAENSRENQLTPWS- 2105

Query: 61   NNVPTDAGGRYFYIREEN-GDFWTPTWMPVRKDLSFFEARHGLGYTKITGERNGLRATIT 119
            N+  TD  G  FY+R+E+ G  ++PT  P+R D   + ARHG GY++   + +G+   + 
Sbjct: 2106 NDPVTDPCGEAFYVRDEDSGALFSPTAQPIR-DTGLYVARHGHGYSRFEHQADGIAMDLL 2164

Query: 120  YFVPRHFTGEVHYLVLENKAEKPRKIKLFSFIEFCLWNALDDMTNF---QRNYSTGEVEI 176
             +VP     ++  L L N +  PR++ +  + E+ L  A      F   +R+ S G    
Sbjct: 2165 EYVPLADPIKISRLTLRNLSAVPRRLSVTRYSEWVLGTARGANAPFIITERDESCG---- 2220

Query: 177  EGSVIYHKTEYRER-RNHYAFYSVNQPIDGFDTDRESFIGLYSGFEAPQAVVEGKP-RNS 234
               ++  +T +        AF  +      +  DR   +G  SG   P A++ G P   +
Sbjct: 2221 ---MLLARTPWSSAFPGRVAFADLGGRQTAWTADRRELLGRNSGPATPAALLTGAPLTGA 2277

Query: 235  VASGWAPIASHYLEIELAPSEKKELIFILGYVENPEEEKWEKPGVINKKRAKEMIEKFKT 294
              +G  P A+    +ELA  E  E+I  +G   + +              A+ ++E+++ 
Sbjct: 2278 TGAGMDPCAALQTRVELAAGESIEIIAFIGQCPSADA-------------ARALVERYRQ 2324

Query: 295  GEDVEHALKELREYWDDLLGRIQVETHDEKLNRMVNIWNQYQCMVTFNISRSASYFESGI 354
              D++  L E+ E+W   LG +QV+T D  ++ M+N W  YQ +     +RSA Y  SG 
Sbjct: 2325 -TDLDAVLLEVTEHWRSALGAVQVKTPDRAMDIMLNGWLLYQTLACRIWARSAFYQASG- 2382

Query: 355  SRGIGFRDSNQDILGFVHMIPEKARQRILDLASIQFEDGSTYHQFQPLTKKGNNEIGGGF 414
                GFRD  QD +      PE  R  IL  AS QF +G   H + P + +G   +    
Sbjct: 2383 --AYGFRDQLQDGMALTFSRPEATRSHILRAASRQFPEGDVQHWWLPHSGQG---VRTRI 2437

Query: 415  NDDPLWLILSTSAYIKETGDWSILGEEVPFDNDPNKK----------------ASLFEHL 458
            +DD +WL  +T+ YI+  GD +IL E V F   P  K                A LFEH 
Sbjct: 2438 SDDRVWLAFATATYIQVAGDATILDEPVTFLEGPLLKPGEHDAFFQPMMAGDAAPLFEHC 2497

Query: 459  KRSFYFTVNNLGPHGLPLIGRADWNDCLNLNCFSKNPDESFQTTVNALDGRVAESVFIAG 518
             R     +   G  GLPLIG  DWND +N                   DG+  ESV++  
Sbjct: 2498 ARGLDQCLELTGELGLPLIGGGDWNDGMNRV---------------GEDGK-GESVWLGW 2541

Query: 519  LFVLAGKEFVEICKRRGLEEEAREAE---KHVNKMIETTLKYGWDGEWFLRAYDAFGRKV 575
            L +   + F  +  +RG   + + AE   KH   + ++  +  WDGEW+ RA    G  +
Sbjct: 2542 LLLRTIELFAPLADQRGTVADVQRAERWRKHAQALADSLEEKAWDGEWYRRATFDDGTWL 2601

Query: 576  GSKECEEGKIFIEPQGMCVMAGIGVDNGYAEKALDSVKKYLDTPY-GLVLQ-QPAYSRYY 633
            GSK+ +E +I    Q   V++G   D   A++A+ SV+++L     GL L   P + +  
Sbjct: 2602 GSKDSDECRIDSIAQSWAVLSG-AADPARAKQAMASVRQHLIREQDGLALLFTPPFDKTE 2660

Query: 634  IELGEISSYPPGYKENAGIFCHNNPWVAIAETVIGRGD---RAFEIYRKITPAYLEDISE 690
             E G I  YPPG +EN G + H   W  +A   +G GD   R F +   I  A   + S 
Sbjct: 2661 KEPGYIKGYPPGLRENGGQYSHAAMWAMLAFAKLGDGDAACRMFSLLNPINHALTPEGSR 2720

Query: 691  IHRTEPYVYAQMVAGKDAPRHGEAKNSWLTGTAAWSFVAITQHILGIRPTYDSLVVDPCI 750
             ++ EPYV A  V G  AP  G    +W TG A W   A  + ILGIR   + L+VDPCI
Sbjct: 2721 RYKVEPYVVAADVYGV-APHKGRGGWTWYTGAAGWMHRAGVEGILGIRREGEWLIVDPCI 2779

Query: 751  PKEWEGFRITRKFRGSIYDITVKNPSHVSKGVKEIIVDGKKIE---GQVLPVFEDGKVHR 807
              +W GF  T     + Y I ++NP+  ++G++   +D + ++   G V    ++G+ H+
Sbjct: 2780 SSQWPGFEATITLGETRYAIRLENPTQANRGIQHAQLDERSLDCTNGWVRLALDEGQ-HQ 2838

Query: 808  V 808
            V
Sbjct: 2839 V 2839


Lambda     K      H
   0.320    0.139    0.431 

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: 4892
Number of extensions: 251
Number of successful extensions: 12
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: 813
Length of database: 2843
Length adjustment: 50
Effective length of query: 763
Effective length of database: 2793
Effective search space:  2131059
Effective search space used:  2131059
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: 60 (27.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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