Alignments for a candidate for cbp in Pandoraea thiooxydans ATSB16

GapMind for catabolism of small carbon sources

Alignments for a candidate for cbp in Pandoraea thiooxydans ATSB16

Align cellobiose phosphorylase (EC 2.4.1.20) (characterized)
to candidate WP_083566737.1 PATSB16_RS08730 phosphorylase

Query= BRENDA::Q9X2G3
         (813 letters)



>NCBI__GCF_001931675.1:WP_083566737.1
          Length = 2916

 Score =  327 bits (838), Expect = 6e-93
 Identities = 239/840 (28%), Positives = 387/840 (46%), Gaps = 75/840 (8%)

Query: 4    GYFDDVNREYVITT---PQTPYPWINYLGTEDFFSIISHMAGGYCFYKDARLRRITRFRY 60
            G F    REYV       +TP PWIN +    F   +S    GY + ++++  ++T +  
Sbjct: 2117 GGFASQGREYVTVLGPDQRTPAPWINVIANPAFGFQVSESGAGYTWSENSQANQLTPWS- 2175

Query: 61   NNVPTDAGGRYFYIRE-ENGDFWTPTWMPVRKDLSFFEARHGLGYTKITGERNGLRATIT 119
            N+   D  G  FY+R+ E G+ W PT +P+R + + + ARHG GY++     +G+ + + 
Sbjct: 2176 NDPVCDTPGEVFYLRDDETGELWAPTALPIRIENTRYIARHGHGYSRFQHSSHGVMSELL 2235

Query: 120  YFVPRHFTGEVHYLVLENKAEKPRKIKLFSFIEFCLWNALDDMTNFQRNYSTGEVEIEGS 179
             FV      ++  L LE+ + +PRK+ +  + E+ L  +      F       E++ +  
Sbjct: 2236 QFVSWSDPVKISVLTLESLSSRPRKLSVTGYAEWVLGTSRAASAPF----IVTEMDAQTG 2291

Query: 180  VIYHKTEYRER-RNHYAFYSVNQPIDGFDTDRESFIGLYSGFEAPQAVVEGKP-RNSVAS 237
             ++    +        AF         +  DR  FIG     E P A+       N   +
Sbjct: 2292 AMFAANPWNAGFGKRIAFVDWVGRKTSWTGDRTEFIGRNGTLEQPAALAGSAGLSNRTGA 2351

Query: 238  GWAPIASHYLEIELAPSEKKELIFILGYVENPEEEKWEKPGVINKKRAKEMIEKFKTGED 297
            G+ P ++    +ELAP ++ +L F+LG   +             +  A+++I +++  + 
Sbjct: 2352 GFDPCSALQTAVELAPGQRVQLTFLLGQTAD-------------RPAARQLIGRYRALDP 2398

Query: 298  VEHALKELREYWDDLLGRIQVETHDEKLNRMVNIWNQYQCMVTFNISRSASYFESGISRG 357
             E  L E+   WD +L ++QVET D   + M+N W  YQ +     +R+A Y  SG    
Sbjct: 2399 TE-VLAEVNAQWDRILTKVQVETPDRATDLMLNGWLLYQVLACRMWARAAFYQASG---A 2454

Query: 358  IGFRDSNQDILGFVHMIPEKARQRILDLASIQFEDGSTYHQFQPLTKKGNNEIGGGFNDD 417
             GFRD  QD +      P+ AR  +LD A+ QF +G   H + P   +G   +    +DD
Sbjct: 2455 YGFRDQLQDCMALNMARPDLARAHLLDAAARQFVEGDVQHWWHPQQGRG---VRTHISDD 2511

Query: 418  PLWLILSTSAYIKETGDWSILGEEVPFDNDPNKKA----------------SLFEHLKRS 461
             LWL    + Y+  T D ++L E +PF   P   A                +LFEH  R+
Sbjct: 2512 RLWLPYVVAQYVSVTADAAVLDEGLPFLEGPAVPAEHEDAYYAPKVSAQTGTLFEHCVRA 2571

Query: 462  FYFTVNNLGPHGLPLIGRADWNDCLNLNCFSKNPDESFQTTVNALDGRVAESVFIAGLFV 521
               ++ N G HGLPL+G  DWND +N                        ESV++     
Sbjct: 2572 IDCSLAN-GAHGLPLMGGGDWNDGMN----------------RVGQAGKGESVWLGWFLY 2614

Query: 522  LAGKEFVEICKRRGLEEEAREAEKHVNKMIETTLKYGWDGEWFLRAYDAFGRKVGSKECE 581
                +F  +   RG         KH   +     K  WDG W+ RAY   G  +GS    
Sbjct: 2615 STIAKFSVLAAARGEHACVERWHKHAAALRAALKKDAWDGAWYRRAYFDDGTPLGSSANA 2674

Query: 582  EGKIFIEPQGMCVMAGIGVDNGYAEKALDSVKKYLDTPYG--LVLQQPAYSRYYIELGEI 639
            E +I    Q   V++G   +     +A+ SV++YL  P    ++L  P + +   + G I
Sbjct: 2675 ECRIDSLAQSWSVISG-AAELARQRRAMASVEQYLIRPGDDLVLLLAPPFDKTPYDPGYI 2733

Query: 640  SSYPPGYKENAGIFCHNNPWVAIAETVIGRGDRAFEIYRKITPA-YLEDISEIH--RTEP 696
              Y PG +EN G + H   W  IA  ++G GDRA ++ + + P  +    + +H  + EP
Sbjct: 2734 KGYLPGVRENGGQYTHAAAWCMIAYAMLGDGDRAGDLLKMLNPVNHASTRAGVHAYKVEP 2793

Query: 697  YVYAQMVAGKDAPRHGEAKN-SWLTGTAAWSFVAITQHILGIRPTYDSLVVDPCIPKEWE 755
            YV A  +    AP H      +W TG+A W +    + +LG++   ++L VDPCIP++W 
Sbjct: 2794 YVVAGDIYA--APAHVRRGGWTWYTGSAGWLYRGGLESVLGLQKHGENLTVDPCIPRDWR 2851

Query: 756  GFRITRKFRGSIYDITVKNPSHVSKGVKEIIVDGKKIEGQV--LPVFEDGKVHRVEVVMG 813
             FR+  +   + Y ITV NP  VSKGV  + +DG  +      + + +DG++HRV V++G
Sbjct: 2852 SFRLDYRHGATHYLITVDNPQGVSKGVARVELDGVPLPSNTHSVALVDDGQLHRVLVMLG 2911



 Score = 55.8 bits (133), Expect = 3e-11
 Identities = 51/217 (23%), Positives = 91/217 (41%), Gaps = 11/217 (5%)

Query: 55   ITRFRYNNVPTDAGGRYFYIREE-NGDFWTPTWMPVRKDLSFFEARHGLGYTKITGERNG 113
            +TR+R  +V  DA G Y ++R+  +GD W+ T+ P+  +   +E        +       
Sbjct: 1658 VTRWR-EDVTCDAWGSYIFLRDTASGDVWSATYQPLGLEPDRYEVVFSEDRARFVRHDGT 1716

Query: 114  LRATITYFVPRHFTGEVHYLVLENKAEKPRKIKLFSFIEFCLWNALDDMTN--FQRNYST 171
            L   +   V      E+  L L N   +  +I+L S+ E  L     D T+  F   +  
Sbjct: 1717 LSTCLEIIVSPEDNAEIRRLTLTNSGAQAVEIELTSYAEVVLAPMAADATHPAFSNLFIH 1776

Query: 172  GEV--EIEGSVIYHK----TEYRERRNHYAFYSVNQPIDGFDTDRESFIGLYSGFEAPQA 225
             E   E+ G +   +    T+      H           G++TDR  F+G       P A
Sbjct: 1777 TEYLPEVHGLLAMRRPHSATDAPVWAAHILAGGSRSENVGYETDRARFLGRGHPIRDPVA 1836

Query: 226  VVEGKP-RNSVASGWAPIASHYLEIELAPSEKKELIF 261
            +++G+P  N+V S   P+ S    +++A     +++F
Sbjct: 1837 IMDGRPLSNTVGSVLDPVLSLRTRVQVAAGATADILF 1873


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: 5509
Number of extensions: 265
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 813
Length of database: 2916
Length adjustment: 51
Effective length of query: 762
Effective length of database: 2865
Effective search space:  2183130
Effective search space used:  2183130
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 24 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 2024 update 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