GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG in Collinsella tanakaei YIT 12063

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate WP_009141894.1 HMPREF9452_RS09360 PTS transporter subunit EIIC

Query= BRENDA::P69786
         (477 letters)



>NCBI__GCF_000225705.1:WP_009141894.1
          Length = 530

 Score =  226 bits (577), Expect = 1e-63
 Identities = 153/524 (29%), Positives = 247/524 (47%), Gaps = 62/524 (11%)

Query: 9   LQKVGKSLMLPVSVLPIAGILLGVGS-----ANFSWLPAV------VSHVMAEAGGSVFA 57
           +QK G ++  PV +   AG+++G G+       F  L A       V +V+ + G +VF 
Sbjct: 5   IQKFGGAMFTPVMLFAFAGVVIGFGTLFTTEVIFGPLAAPGTMWYGVWNVILQGGWTVFN 64

Query: 58  NMPLIFAIGVALGFTNNDG----VSALAAVVAYGIMVKTMA----------VVAPLVLHL 103
            +PL+FA+ + +G  N       + AL   + +   V TM             A +    
Sbjct: 65  QLPLLFAVSLPIGLANKQNARCCMEALVGYLTFQYFVSTMLSQWGGFFGVDFAAEVGGTS 124

Query: 104 PAEEIASKHLADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIF 163
               IAS    D G++G +    I   + N+FY ++LPE+LG FAG  FV II+    + 
Sbjct: 125 GLAMIASIKTLDMGMIGALAVSGIIIAIHNKFYEVELPEWLGVFAGSTFVYIITFFVMLP 184

Query: 164 TGVVLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIG 223
              V    WP +   I+ F  + A     +  G++ F+ER L+PFGLHH+   PF     
Sbjct: 185 VAFVACLGWPHVQDGIRAFQGFVATTG-TLGVGVFAFLERALIPFGLHHLMYSPFYYDNA 243

Query: 224 EYTNAAGQVFHGDIPRYMAGDPTAGKLSGGFLF------KMYGLPAAAIAIWHSAKPENR 277
                    F   +P+  A   +  +L+    F      K++G P  A+A + +AKPE +
Sbjct: 244 VVDGGIYTAFATALPQIAASTDSLKELAPYAAFTCSTWSKIFGCPGIALAFFVTAKPEKK 303

Query: 278 AKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGL---AFPICILLGMRDG 334
            ++  ++I   LT+   G+TEPIEF+F+F+AP L+I+H +LA L   A  +   +G+  G
Sbjct: 304 KELLSLLIPITLTAVFCGVTEPIEFTFLFIAPPLFIVHCVLAALLAMAINMVGCVGVFAG 363

Query: 335 TSFSHGLIDFIVLSGNSSKLWLFP-IVGIGYAIVYYTIFRVLIKALDLKTPGREDATEDA 393
                  ++FI L  N  + +    +VG+ + ++++ +FR LI   D KTPGRED  E  
Sbjct: 364 GIIEISSLNFIPLMANHWQQYAMALVVGLVFTVIWFVVFRFLIVKFDFKTPGREDDDEQV 423

Query: 394 KATGTSE-------------------------MAPALVAAFGGKENITNLDACITRLRVS 428
           K    +E                         MA  ++   GG +NI ++  C+TRLRV+
Sbjct: 424 KFRSKAEYRAAKNGELASGEGAKVDESDPYAVMAAEVLELLGGADNIVDVTNCVTRLRVN 483

Query: 429 VADVSKV-DQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMD 471
           V D + V D    K +G +G+   G G+Q I G K   ++   +
Sbjct: 484 VKDETLVADDPDFKSIGTSGIAKNGKGMQVIIGLKVPKVRDRFE 527


Lambda     K      H
   0.325    0.140    0.422 

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: 648
Number of extensions: 36
Number of successful extensions: 8
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: 477
Length of database: 530
Length adjustment: 34
Effective length of query: 443
Effective length of database: 496
Effective search space:   219728
Effective search space used:   219728
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: 40 (21.6 bits)
S2: 52 (24.6 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