Alignments for a candidate for BT0355 in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for BT0355 in Echinicola vietnamensis KMM 6221, DSM 17526

Align Na+/glucose cotransporter (characterized, see rationale)
to candidate Echvi_1680 Echvi_1680 transporter, SSS family

Query= uniprot:Q8AAV7
         (564 letters)



>FitnessBrowser__Cola:Echvi_1680
          Length = 528

 Score =  283 bits (724), Expect = 1e-80
 Identities = 169/535 (31%), Positives = 302/535 (56%), Gaps = 43/535 (8%)

Query: 1   MEALDWLVIGVFFLALIGIIVWVVRQKQNDSAD-YFLGGRDATWLAIGASIFASNIGSEH 59
           ++ LD+ V+G++ + LIGI  WV  +K+ D+ +  FL G    W +IG +++ +N+G   
Sbjct: 7   LQPLDFAVLGLYLVTLIGIGYWVSFKKKRDADENLFLAGNSLGWPSIGFTMWGTNVGPSM 66

Query: 60  LIGLAGAGASSGMAMAHWEIQGWM-ILILGWVFVPFYSRSMVYTMPEFLERRYNPQSRTI 118
           LI  A  G ++G+   ++    ++ I +L  VF P Y  + V T+PEF+ +R+   ++ I
Sbjct: 67  LIASASIGYTTGVVAGNFAWYAFIFIFLLAVVFAPRYLGARVQTLPEFMGKRFGSSTQNI 126

Query: 119 LSVISLVSYVLTKVAVTVYAGGLVFQQVFGIKELWGIDFFWIAAIGLVVLTALYTIFGGM 178
           L+  ++V+ +++ +++T++AGG++ +Q+  +         W++ + L+++ A +TI GG+
Sbjct: 127 LAWYTIVTVLISWLSLTLFAGGILIRQILDLP-------LWLSVVILILIAAFFTIAGGL 179

Query: 179 KSVLYTSVLQTPILLLGSLIILVLGFKELGGWDEMMRVCGAVTVNDYGDTMTNLIRSNDD 238
           K++ YT+V Q  +L++ SL + + G  ++GG  E++    A T  +Y     NL+   DD
Sbjct: 180 KAIAYTNVFQMVLLIVVSLALTLTGLYKVGGVGELI----ANTPGEYW----NLLLPADD 231

Query: 239 ANFPWLGALIGSAIIGFWYWCTDQFIVQRVLSGKNEKEARRGTIFGAYLKLLPVFLFLIP 298
            N+PW+   +G  ++G W+WCTDQ +VQ VL  KN KE + G  F  +LK+L V LF+IP
Sbjct: 232 PNYPWVAIALGYPVMGVWFWCTDQSMVQSVLGAKNLKEGQLGANFTGWLKILDVALFIIP 291

Query: 299 GMIAFALHQKYIGAGGEGFLPMLANGTANADAAFPTLVAKLLPAGVKGLVVCGILAALMS 358
           G+I + L             P L     N D A+ T+V KL P G+ GLV+  ++AAL+S
Sbjct: 292 GIICYVL------------FPDL----DNPDEAYMTMVTKLFPVGMTGLVMAVLIAALVS 335

Query: 359 SLASLFNSSAMLFTIDFY-KRFRPETPEKKLVGIGQIATVVIVILGI-LWIPIMRSVGDV 416
           ++ S  N+ + +FT+D Y K+++PE  +K++V IG++ TV+  ++ I L + I    G  
Sbjct: 336 TIDSALNALSTVFTMDIYVKKYKPEATQKQIVTIGRVVTVLGAVIAIFLTLAIDSIKGLN 395

Query: 417 LYTYLQDVQSVLAPGIAAAFLLGICWKRTSAQGGMWGLIAGMIIGLTRLGAKVYYSNAGE 476
           L+   Q +   +AP ++  FL G+ WK+T+ +     L+ G I+    LG  V Y     
Sbjct: 396 LFDVFQSILGFIAPPMSVVFLFGVLWKKTTTKAANTVLLFGTILS---LGIGVLYLWVFP 452

Query: 477 VADSTFKYLFYDMNWLFFCGWMFLFCIIVVIVVSLATEAPTAEKIQGLVFGTATK 531
            A+    Y F+  ++L    ++F+F   +++V+S          +  L +GT  K
Sbjct: 453 NAE----YAFWP-HFLLLSFYIFVFLAALIVVISYVERNRKDLHVSTLDYGTIPK 502


Lambda     K      H
   0.328    0.142    0.454 

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: 928
Number of extensions: 48
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: 564
Length of database: 528
Length adjustment: 35
Effective length of query: 529
Effective length of database: 493
Effective search space:   260797
Effective search space used:   260797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. 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)
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, or view the source code.

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