GapMind for catabolism of small carbon sources

 

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

Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_043917160.1 jaqu_RS01450 TRAP transporter large permease

Query= reanno::SB2B:6938090
         (466 letters)



>NCBI__GCF_000877395.1:WP_043917160.1
          Length = 424

 Score =  253 bits (646), Expect = 9e-72
 Identities = 163/465 (35%), Positives = 248/465 (53%), Gaps = 53/465 (11%)

Query: 1   MTIATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAI 60
           MT+A + + LF+ +LLG+P+A ALG   M  +LL+  D    +A +   +T   + LLA+
Sbjct: 1   MTLALVVICLFVLLLLGVPVAFALG--GMGLVLLWLGDFSLLMAPQGIMSTLNGFILLAV 58

Query: 61  PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120
           P F+L    L  GGV R +       VGH  GGLA+A++++C LFAA+SGSS AT A IG
Sbjct: 59  PLFLLMGNVLLKGGVGRDLFAAVQAWVGHWPGGLAVATILSCGLFAAISGSSVATAATIG 118

Query: 121 SIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180
           ++ I  M + GY ++   G++   GTLGILIPPSI M+VY    E S   +FMAG+ PGL
Sbjct: 119 TVAIPEMTKRGYDKRHTYGLLAAGGTLGILIPPSIPMIVYGFVAEQSVIALFMAGIGPGL 178

Query: 181 -LMGVLLMVAIYIVARIKNLPSRPFPGVKAL--------SLSSAKAMGGLALIFIVLGSI 231
            L+G  ++ AI        L +R  PG + L          +S +A+  +AL  +V+  I
Sbjct: 179 ALIGAFIVFAI--------LHARFSPGYERLRPAPWSERRAASIRALPSVALAALVVFGI 230

Query: 232 YGGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLI 291
           Y G  +PTEAAA+    A ++ V                                   ++
Sbjct: 231 YSGAFTPTEAAAIGFAAALVITVV----------------------------------IL 256

Query: 292 KTPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFL 351
           +T T +      RD    ++ +L I+A A +F   L   R+P  I+  I      P  F+
Sbjct: 257 RTLTWQAFVESARDAMVTTVAILLIVAGAKVFGKALALWRVPQDISAFIGATIDGPIMFI 316

Query: 352 IIVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGL 411
           ++V+++LL  G   E  +++LIM P+L P A+ LG DPI  GI MV+ +E  ++TPPVGL
Sbjct: 317 LVVSVVLLLMGLIFEALSMVLIMTPVLLPAAMGLGFDPIWFGIYMVIMVECALITPPVGL 376

Query: 412 NLFVTAGITGRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLP 456
           NL+V   +   ++  V    LP+L ++L  +VL+   P ++L+LP
Sbjct: 377 NLYVIQSVACATLADVARGTLPFLGIMLASVVLLYAWPDLALYLP 421


Lambda     K      H
   0.329    0.144    0.424 

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: 585
Number of extensions: 38
Number of successful extensions: 5
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: 466
Length of database: 424
Length adjustment: 32
Effective length of query: 434
Effective length of database: 392
Effective search space:   170128
Effective search space used:   170128
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