GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ectP in Pseudomonas litoralis 2SM5

Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate WP_090271580.1 BLU11_RS00755 BCCT family transporter

Query= SwissProt::Q87PP5
         (562 letters)



>NCBI__GCF_900105005.1:WP_090271580.1
          Length = 685

 Score =  389 bits (998), Expect = e-112
 Identities = 203/501 (40%), Positives = 312/501 (62%), Gaps = 11/501 (2%)

Query: 61  WGFDIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLL 120
           W   I  PVF I +   +  L+     +P  A +  + + + I   F  F+M S   FL+
Sbjct: 10  WNTTILLPVF-IPSFFFILLLVISTATQPELAGELFSSVLSYITTTFGWFYMLSVAIFLV 68

Query: 121 FAVGLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGT 180
           F V +  S  G I+LG   A P +S  +W +MLF+AG GI LLF+ VAEP  ++ +    
Sbjct: 69  FIVIVAMSKWGHIKLGPDHAEPQYSFPAWFAMLFSAGYGIALLFFGVAEPVLHYAE---P 125

Query: 181 PLNAEAYSADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYPIFG 240
           P  AE  + DA   AM    FHWG H W+IY L  L LA+F+F  GLPLS+R+A YP+ G
Sbjct: 126 PQGAEGLTVDAAKQAMQIAFFHWGFHIWAIYGLTGLVLAYFSFRHGLPLSIRSALYPLIG 185

Query: 241 DRAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVF-GLNGGIGTQMVVIAFVT 299
           DR +G +GH +D  A+L T+FG+AT+LGL   Q  +G+N+++  +  GIG Q+  IAF+T
Sbjct: 186 DRIYGPIGHAVDTFAILGTMFGIATTLGLSVAQINAGLNYLWPSIPIGIGVQVGTIAFIT 245

Query: 300 FIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITFI-TFDTAMGSLVDTTMAYIQNIIPL 358
           F+ + SV+ G+D G+K LS +NMIVA +L++F+ F       + + +  T +Y+ NI+  
Sbjct: 246 FLTMGSVIAGMDKGIKNLSMLNMIVATSLMLFVFFAGPTIFILEAFLQNTGSYLNNIVER 305

Query: 359 S-NPHGREDETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLFAVIVIPTLVTL 417
           + N        W+  WT+F + W ++W+PFVG+FIA++S+GRT+R+F+F V+++PT+ T 
Sbjct: 306 TFNLQAYSRSDWIGNWTLFIFGWTIAWAPFVGLFIAKISRGRTIRQFVFGVMLVPTIFTF 365

Query: 418 VWMSVFGGIALDQVVNK-VGELGANGLTDISLTLFHVYDVLPYSSVISILSIVLILVFFI 476
            W SVFG  AL  ++N+    L      D ++ LF +++ LP +++IS ++++LI +FFI
Sbjct: 366 FWFSVFGDTALHLIINQGYSVLIDQVQADNAIALFKLFEQLPMTAIISTITVILITLFFI 425

Query: 477 TSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGKEALQALQSGVVATG 536
           TS+DSG+LV+DS+ +GG +  P  QR FWA + G +A+V+L  GG   L+ALQS  VA+ 
Sbjct: 426 TSADSGALVVDSLASGGALVTPAWQRGFWAILSGVLASVLLVAGG---LKALQSMAVASA 482

Query: 537 LPFTFVLLLMCVSLVKGLRTE 557
           LPF  ++L+  V + + L  E
Sbjct: 483 LPFAVIMLISAVGMWRALTIE 503


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: 1012
Number of extensions: 54
Number of successful extensions: 6
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: 685
Length adjustment: 37
Effective length of query: 525
Effective length of database: 648
Effective search space:   340200
Effective search space used:   340200
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: 53 (25.0 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