GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gamP in Collinsella tanakaei YIT 12063

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate WP_009141894.1 HMPREF9452_RS09360 PTS transporter subunit EIIC

Query= SwissProt::P39816
         (631 letters)



>NCBI__GCF_000225705.1:WP_009141894.1
          Length = 530

 Score =  229 bits (584), Expect = 2e-64
 Identities = 166/533 (31%), Positives = 261/533 (48%), Gaps = 72/533 (13%)

Query: 7   QILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNI----------------PIIKDAGGVV 50
           Q +Q+ G A+ TPV +   AG+++ FG      +                 +I   G  V
Sbjct: 3   QKIQKFGGAMFTPVMLFAFAGVVIGFGTLFTTEVIFGPLAAPGTMWYGVWNVILQGGWTV 62

Query: 51  FDNLPLIFAVGVAIGLAGGEGV-AGLAAVIGYL----ILTVTLDNMGKLLGLQPPYE--G 103
           F+ LPL+FAV + IGLA  +     + A++GYL     ++  L   G   G+    E  G
Sbjct: 63  FNQLPLLFAVSLPIGLANKQNARCCMEALVGYLTFQYFVSTMLSQWGGFFGVDFAAEVGG 122

Query: 104 AEHL--------IDMGVFGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSS 155
              L        +DMG+ G + +  +   ++ +F  +EL   LG F+G  FV IIT    
Sbjct: 123 TSGLAMIASIKTLDMGMIGALAVSGIIIAIHNKFYEVELPEWLGVFAGSTFVYIITFFVM 182

Query: 156 LVIGVIFSFVWPLIQNGINAASSLIADS-TVGLFFYATIYRLLIPFGLHHIFYTPFYFMM 214
           L +  +    WP +Q+GI A    +A + T+G+  +A + R LIPFGLHH+ Y+PFY+  
Sbjct: 183 LPVAFVACLGWPHVQDGIRAFQGFVATTGTLGVGVFAFLERALIPFGLHHLMYSPFYYDN 242

Query: 215 -----GEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPE 269
                G YT  +T        T           F    +  +  C P +ALA   TA+PE
Sbjct: 243 AVVDGGIYTAFATALPQIAASTDSLKELAPYAAFTCSTWSKIFGC-PGIALAFFVTAKPE 301

Query: 270 KKKMISGVMISAALTSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGY 329
           KKK +  ++I   LT++  G+TEP+EF+FLF+AP L++++ +LA ++ +  ++  V    
Sbjct: 302 KKKELLSLLIPITLTAVFCGVTEPIEFTFLFIAPPLFIVHCVLAALLAMAINM--VGCVG 359

Query: 330 TFSGGGIDY-VLNY-GLSTNGW----VVIPVGIVFAFIYYYLFRFAILKWNLKTPGRETD 383
            F+GG I+   LN+  L  N W    + + VG+VF  I++ +FRF I+K++ KTPGRE D
Sbjct: 360 VFAGGIIEISSLNFIPLMANHWQQYAMALVVGLVFTVIWFVVFRFLIVKFDFKTPGREDD 419

Query: 384 -----------------------EDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDACI 420
                                  E  + +E  P A   +A  VL+ LGG  NI ++  C+
Sbjct: 420 DEQVKFRSKAEYRAAKNGELASGEGAKVDESDPYA--VMAAEVLELLGGADNIVDVTNCV 477

Query: 421 TRLRVTVHQPSQVCKD-ELKRLGAVGVLEVNNNFQAIFGTKSDALKDDIKTIM 472
           TRLRV V   + V  D + K +G  G+ +     Q I G K   ++D  + ++
Sbjct: 478 TRLRVNVKDETLVADDPDFKSIGTSGIAKNGKGMQVIIGLKVPKVRDRFEALL 530


Lambda     K      H
   0.324    0.142    0.421 

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: 823
Number of extensions: 45
Number of successful extensions: 7
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: 631
Length of database: 530
Length adjustment: 36
Effective length of query: 595
Effective length of database: 494
Effective search space:   293930
Effective search space used:   293930
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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