Alignments for a candidate for cbp in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for cbp in Thiothrix lacustris DSM 21227

Align cellobiose-phosphorylase (CepA) (EC 2.4.1.20) (characterized)
to candidate WP_028488141.1 Q394_RS0103990 glucoamylase family protein

Query= CAZy::CAB16926.1
         (813 letters)



>NCBI__GCF_000621325.1:WP_028488141.1
          Length = 2852

 Score =  332 bits (850), Expect = 2e-94
 Identities = 246/835 (29%), Positives = 398/835 (47%), Gaps = 76/835 (9%)

Query: 4    GYFDDKNREYVIVTPR----TPYPWINYLGTEDFFSIISHMAGGYCFYKDARLRRITRFR 59
            G F    REYV+ TP     TP PW+N L    F ++IS     Y + ++A   R+T + 
Sbjct: 2060 GGFTADGREYVM-TPAADQTTPAPWVNVLANPHFGTVISESGQAYTWRENAHEYRLTPW- 2117

Query: 60   YNNVPTDAGGRYFYIREED-GDFWSPTWMPVRRDLSFFEARHGLGYTKIAGDINGLRATI 118
            +N+  +D  G   Y+R+ED G+FWSPT +P     ++  +RHG GY+    + NG+ + +
Sbjct: 2118 HNDPVSDLSGEALYLRDEDSGEFWSPTALPCPGAGAYI-SRHGFGYSVFEHNENGIYSEL 2176

Query: 119  TFFVPRHFTGEVHHLVLQNRTERPRRIKLFSFIEFCLWNALDDMTNFQRNYSTGEVEIEG 178
            T  V    + +   L ++N + R R++    ++E+     L D+T     +   E     
Sbjct: 2177 TVCVALDASVKFSVLKVRNASGRTRQLSATGYVEW----VLGDLTPKSAPHIITECTAPI 2232

Query: 179  SVIYHKTEYR-ERRNHYAFYSVNHSIDGFDTDRESFMGLYNGFEAPQAVVEGNPRNSVAS 237
              ++ +  Y  E     AF++V+     F  DR  F+G       P A+        V +
Sbjct: 2233 GALFARNPYSMEFAERVAFFAVDDRNHTFTGDRAEFIGRNGTLRHPAALQRAYLSGKVGA 2292

Query: 238  GWAPIASHYLELEIPPLGEKELIFILGYVENPEEEKWERPGVINKKRAKEMIERFKTGED 297
               P A+  +  E+    E+E++F LG   +  +             A+ ++ RF+  E 
Sbjct: 2293 ALDPCAAIQVSFELAAGHEREIVFKLGAGRDMHD-------------AQALVHRFRGVEA 2339

Query: 298  VERALKELKEYWDELLGRIQVETHDEKLNRMVNIWNQYQCMVTFNIARTSSYFESGISRG 357
               ALK++++YW + L  +QVET D  +N + N W  YQ +      R S Y++SG    
Sbjct: 2340 TRNALKQVQDYWVKTLSTVQVETPDAAVNMLANGWLLYQTLGCRLWGR-SGYYQSG--GA 2396

Query: 358  IGFRDSNQDILGFVHMIPEKARQRILDLASIQFEDGSTYHQFQPLTKKGNNEIGGGFNDD 417
             GFRD  QD++  VH  P+K R+ +L  A  QF +G   H + P + +G   +    +DD
Sbjct: 2397 FGFRDQLQDVMALVHAEPDKVREHLLLCAGHQFAEGDVQHWWHPPSDRG---VRTQCSDD 2453

Query: 418  PLWLILSTSAYIKETGDWSILNEEVPF----------DNDPD------KKATLFEHLKRS 461
             LWL L T  YI  TGD+S+L+E+  F          D+  D      + A+L++H  R+
Sbjct: 2454 YLWLPLVTCRYILTTGDYSVLDEQRGFLSGRAVNAGEDSYYDLPGHSAEVASLYQHCVRA 2513

Query: 462  FYFTVNNLGPHGLPLIGRADWNDCLNLNCFSKNPDESFQTTVNALDGRVAESVFIAGLFV 521
                +  LG HGLPL+G  DWND +NL                 ++G+  ES+++     
Sbjct: 2514 ILHGLR-LGEHGLPLMGSGDWNDGMNLV---------------GIEGK-GESIWLGFFLC 2556

Query: 522  LAGKEFVEICRRLGLEDEAKEAEKHVKKMIETTLEYGWDGEWFLRAYDAFGRKVGSKECE 581
                +F E+ R       A+  ++   ++ +    +GWDG W+ RAY   G  +GS    
Sbjct: 2557 EVLGQFAELARLHNDIPFAERCQQERYQLHQNLERHGWDGAWYRRAYFDDGTPLGSSTNP 2616

Query: 582  EGKIFIEPQGMCVMAGIGVENGYAKKALDSVKEHL--DTHYGLVLQQPAYSRYYIELGEI 639
            E +I    Q   V++GIG     + +A+ S+  HL    H  + L  P ++   +  G I
Sbjct: 2617 ECQIDSIAQSWSVLSGIGSPER-SLQAMQSLNTHLVRRDHALVQLLDPPFNTSDLNPGYI 2675

Query: 640  SSYPPGYKENAGIFCHNNPWVAIAESVIGRGDRAFEIYRKITPAY---LEDISEIHRTEP 696
              Y PG +EN G + H   W A+A + +G  +RA+E+   I P       D    ++ EP
Sbjct: 2676 RGYVPGVRENGGQYTHAAIWAAMAFARLGDSERAWELLGMINPVNHGTSADGIATYKVEP 2735

Query: 697  YVYAQMVAGKDAPRHGEAKNSWLTGTAAWSFVAITQYILGVRPTYDGLMVDPCIPEDWDG 756
            YV A  V G  AP  G    +W TG+A+W +  IT+ +LG+R   D L  +P +P+DW  
Sbjct: 2736 YVVAADVYGI-APHTGRGGWTWYTGSASWMYRLITESLLGLRREGDSLRFEPSLPQDWST 2794

Query: 757  FKITRRFRGATYEITVKNPHHVSKGVKEIIVDGKKIEGQVLPVFNDGKVHRVEVL 811
            FK+  R+R   Y I ++       G   + +DG + +   +P+ +D   H+V VL
Sbjct: 2795 FKMRYRYRETVYHIIIQQ----VVGAASVSLDGLEQQNGSIPLVDDRVEHQVTVL 2845



 Score = 49.3 bits (116), Expect = 3e-09
 Identities = 57/268 (21%), Positives = 106/268 (39%), Gaps = 15/268 (5%)

Query: 14   VIVTPRTPYPWINYLGTEDFFSIISHMAGGYCFYKDARLRRITRFRYNNVPTDAGGRYFY 73
            V+  P T  P +  L    +  ++++  GGY   KD     +TR+ + +   D  G + Y
Sbjct: 1565 VLNNPNTLLPEVQLLSNGHYHVMVTNAGGGYSRCKDL---AVTRW-HEDTTRDHWGTFCY 1620

Query: 74   IRE-EDGDFWSPTWMPVRRDLSFFEARHGLGYTKIAGDINGLRATITFFVPRHFTGEVHH 132
            IR+   G FWS    P       +EA    G  +     +     +   V      E+  
Sbjct: 1621 IRDVASGVFWSTAHQPTLAPAEHYEAIFSEGRAEFRRRDHDFDTHLDIVVSPEDDIELRR 1680

Query: 133  LVLQNRTERPRRIKLFSFIEFCLWNALDDMTN--FQRNYSTGEV--EIEGSVIYHKTEYR 188
            + + N +   R I++ S+ E  L +A  D  +  F + +   E+   ++  +   +    
Sbjct: 1681 VRITNDSPLRRTIEVTSYAEVVLASAASDTLHPAFSKLFVQTEIVDPLQAILCTRRPRAL 1740

Query: 189  ERRNHYAFYSVN-HSID----GFDTDRESFMGLYNGFEAPQAVVEGNP-RNSVASGWAPI 242
            +  + + F+ +  H  D     ++TDR  F+G      AP A+   +   NSV +   PI
Sbjct: 1741 DEHSPWLFHLMAVHEGDSNGISYETDRAQFIGRGKTLVAPHAMTAADHLSNSVGAVLDPI 1800

Query: 243  ASHYLELEIPPLGEKELIFILGYVENPE 270
             +    + + P     L  ++G     E
Sbjct: 1801 VAIRHRITLEPEASVTLDMVIGIAATRE 1828


Lambda     K      H
   0.321    0.140    0.435 

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: 5370
Number of extensions: 267
Number of successful extensions: 13
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: 813
Length of database: 2852
Length adjustment: 50
Effective length of query: 763
Effective length of database: 2802
Effective search space:  2137926
Effective search space used:  2137926
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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