Alignments for a candidate for ectP in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ectP in Halomonas desiderata SP1

Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate WP_086509110.1 BZY95_RS06250 BCCT family transporter

Query= SwissProt::Q87PP5
         (562 letters)



>NCBI__GCF_002151265.1:WP_086509110.1
          Length = 524

 Score =  613 bits (1582), Expect = e-180
 Identities = 304/513 (59%), Positives = 386/513 (75%), Gaps = 5/513 (0%)

Query: 47  DTTDYQVGQDNVQKWGFDIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQ 106
           D    + GQDN Q  G D H+PVF +SA L +   I   L+ P  A   L   +   IE 
Sbjct: 5   DAPILEPGQDNAQVLGMDFHHPVFPLSA-LAILAFILYALIYPDAANSHLTAARGFSIEH 63

Query: 107 FDAFFMWSTNFFLLFAVGLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWS 166
           FD  FM + N F+L  + L+  PLG+IRLGG +A P++ST SW +MLFAAGMGIGL+FWS
Sbjct: 64  FDWLFMIAGNLFVLLCLTLIVLPLGRIRLGGSQARPEYSTTSWFAMLFAAGMGIGLMFWS 123

Query: 167 VAEPTAYFTDWWGTPLNAEAYSADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKG 226
           VAEP AY+TDW+GTPLNAEA++    S A+GATMFHWG+H W+IY +V L+LAFFA+N+G
Sbjct: 124 VAEPVAYYTDWYGTPLNAEAHTPAGASAAIGATMFHWGLHPWAIYGVVGLSLAFFAYNRG 183

Query: 227 LPLSLRAAFYPIFGDRAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNG 286
           LPL+LR+AF PI G+R  GW GH+IDI+AVL+T+FGLATSLG GA QA  G+N+++G+  
Sbjct: 184 LPLTLRSAFTPILGERVRGWFGHIIDIVAVLATIFGLATSLGFGASQAAGGLNYLWGVPN 243

Query: 287 GIGTQMVVIAFVTFIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITFITFDTAM--GSL 344
            IGTQ+ +I  VT +A+ SV RGIDGGVKL S +NM++A  LL F+  +T    +   +L
Sbjct: 244 TIGTQLAIIVVVTAVALFSVWRGIDGGVKLFSKINMMLALGLLTFV-LVTGGVLLFVNNL 302

Query: 345 VDTTMAYIQNIIPLSNPHGREDETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREF 404
             TT+AY+ +I+PLSN  GR+D TW HGWTVFYWAWW+SWSPFVGMFIARVS+GRTVREF
Sbjct: 303 WHTTLAYVSHIVPLSNWVGRDDTTWYHGWTVFYWAWWISWSPFVGMFIARVSRGRTVREF 362

Query: 405 LFAVIVIPTLVTLVWMSVFGGIALDQVVNKVGELGANGLTDISLTLFHVYDVLPYSSVIS 464
           L AV+++PTLVTLVWMS FGG AL+Q    VG L A+G++D+SL +F + + LP +++ S
Sbjct: 363 LIAVLLVPTLVTLVWMSAFGGTALNQSAAGVGAL-ADGISDVSLAMFQMLEHLPLTTLTS 421

Query: 465 ILSIVLILVFFITSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGKEA 524
            L+I+L+L+FFITSSDSGSLVID+ITAGGK DAP  QR+FWA +EG IA ++L+ GG  A
Sbjct: 422 SLAILLVLIFFITSSDSGSLVIDNITAGGKTDAPRGQRVFWAVLEGVIAGILLYGGGSTA 481

Query: 525 LQALQSGVVATGLPFTFVLLLMCVSLVKGLRTE 557
           L ALQ+G VATGLPFT VLL M   LVKGLR E
Sbjct: 482 LGALQAGAVATGLPFTLVLLGMAYCLVKGLREE 514


Lambda     K      H
   0.327    0.141    0.445 

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: 1026
Number of extensions: 65
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: 562
Length of database: 524
Length adjustment: 35
Effective length of query: 527
Effective length of database: 489
Effective search space:   257703
Effective search space used:   257703
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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
the source code
instructions for running GapMind on your computer

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