GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Jannaschia aquimarina GSW-M26

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_043919376.1 jaqu_RS12740 TRAP transporter large permease

Query= uniprot:I7DRS6
         (467 letters)



>NCBI__GCF_000877395.1:WP_043919376.1
          Length = 457

 Score =  240 bits (612), Expect = 8e-68
 Identities = 154/468 (32%), Positives = 246/468 (52%), Gaps = 35/468 (7%)

Query: 3   VVLLFSMVIGLL-LIGVPIAVALG--LSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLA 59
           +V + S+ + +L ++GVP+ + +G  +    F+L      L ++   L + F   F LLA
Sbjct: 6   IVTMISIGVTILFMLGVPVFLVIGWWVVGMSFVL---GLPLLNIGAALSDVFTDGFALLA 62

Query: 60  IPFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAI 119
           +P FIL    +   G+ARR+  F+ +C+G + GGLA+A + AC LFAA+SGS+ AT   I
Sbjct: 63  MPLFILTGDLINRSGIARRLSDFAYSCLGWIRGGLAMASIGACGLFAAISGSNSATTATI 122

Query: 120 GSIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPG 179
           GS++   M + GY + F+A      GTLGI+IPPSI+ +VY   + + +  +F+AG++PG
Sbjct: 123 GSMLHPEMTKGGYDERFSAATAAAGGTLGIIIPPSIIFIVYGFLLNLPISDLFVAGILPG 182

Query: 180 -LMAGLMLMVTIYVMAKVKNLPKGEWLGWG--------EVAASAANASVGLLLIGIILGG 230
            LMAG M+     V  +          GWG         V  +   A +G   IG++L G
Sbjct: 183 ILMAGAMMTACFIVCWR---------NGWGILIGLSPARVIKTGIGAWLGFFAIGLVLWG 233

Query: 231 IYGGIFTPTEAAAVA---SVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTV 287
           IY G F+PTEAA V     +   F+   +Y+ M   +   KP+D         +ML    
Sbjct: 234 IYTGKFSPTEAAGVTVGFCIIVGFLCLPLYKLM-HRRDGEKPEDRAIEERGFAEML---- 288

Query: 288 VYFIPSFFHADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGP 347
              +  F   +       + ++T  L  +IA +++++ +L+     + I+  + S G G 
Sbjct: 289 --LVQGFGPTELPSITMRSAQITGILAPLIAVSVVMQQILSVLGAQEAISAFVTSMG-GY 345

Query: 348 VMFLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITP 407
              L     I+ + G  +E   + +I+AP++ PIA  +G+DPI   +I +V   IG ITP
Sbjct: 346 HAVLFTAMAIVFVSGMVLESLPVTIILAPILAPIAAGVGVDPIQFAVIFLVGASIGFITP 405

Query: 408 PVGLNLFVTSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVL 455
           P GLNL+V SGV G+P   ++R  LP+L  L +    I  +P +ST L
Sbjct: 406 PYGLNLYVASGVTGVPYFRLLRYILPYLVALILAWFTIALVPGLSTAL 453


Lambda     K      H
   0.329    0.144    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: 618
Number of extensions: 30
Number of successful extensions: 2
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: 467
Length of database: 457
Length adjustment: 33
Effective length of query: 434
Effective length of database: 424
Effective search space:   184016
Effective search space used:   184016
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 (21.8 bits)
S2: 51 (24.3 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