GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ectP in Phaeobacter inhibens BS107

Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate GFF3740 PGA1_262p01440 BCCT transporter

Query= SwissProt::Q87NZ5
         (553 letters)



>FitnessBrowser__Phaeo:GFF3740
          Length = 514

 Score =  254 bits (650), Expect = 4e-72
 Identities = 173/513 (33%), Positives = 262/513 (51%), Gaps = 55/513 (10%)

Query: 41  IHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGNVF------- 93
           I+  +F +SG  I LF VA L           GL A +    DW F  +   F       
Sbjct: 15  INKPLFLLSGGFIALFCVAALVNLD-------GLSALV----DWGFNIAATYFGLYWQIL 63

Query: 94  ----VIVCLVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHF 149
                ++ LVL + P GR  +GG  ATP+++   W +M+    +  G VF+   EP++HF
Sbjct: 64  LLATFLIGLVLCILPGGRAIMGGL-ATPEFTTFQWGSMIMCTLLAGGGVFWAAGEPIAHF 122

Query: 150 SSALGGVNIENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAI- 208
             +               PL GA G ++AA    +A +  HW    W+I   L+  + + 
Sbjct: 123 LYS--------------PPLYGAEGGSEAAVTPAIAQSFMHWGFLAWAILGSLSTVMLMH 168

Query: 209 FSFNKGLPLTMRSIFYPLFGER-VWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLN 267
           + + KGLPL  R++ YP+FG++ + G +G I D  +++A V G    +G+   Q + GL+
Sbjct: 169 YHYEKGLPLAPRTLLYPVFGDKAINGPIGVIADASSIIAVVAGTVGPIGFLGLQVSYGLS 228

Query: 268 FLFGVPMTDTTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTM 327
            LFG+P    TQ V+I  + AL  IS + GL  G++ LS+IN+ILAA+LL +V++ GPT 
Sbjct: 229 DLFGIPDVFATQFVVIGALVALYTISAMTGLSRGIQLLSKINVILAAVLLIYVLLAGPTG 288

Query: 328 AILTGFFDNIASYITNIPALSMPFEREDV------NYSQGWTAFYWAWWISWSPFVGMFI 381
            I   FF   A+Y+ N     M   R D        +   WT F+W W++ + P + MFI
Sbjct: 289 FIFGSFFSGFATYLGNF--FQMALYRGDAAVFGAPGWLGWWTVFFWGWFMGYGPLMAMFI 346

Query: 382 ARVSRGRSVREFIICVILIPSTVCVLWMTAFGGTAISQYVND--GYEAVFNA-ELPLKLF 438
           ARVSRGRS+R  II + +I   V   W T  GGT I+  + +     A F    LP  L 
Sbjct: 347 ARVSRGRSIRSIIIMLSIIAPIVTNFWFTIIGGTGIAMELAEPGTVSAAFEGFNLPAALL 406

Query: 439 AMLDVMPFAEITSVVGIILVVVFFITSSDSGSLVIDTIAAGGKVDAP-TPQRVFWCTFEG 497
           A+ + +P   + S++ +IL  +F  T+ DS S VI      G  D P T  RVFW    G
Sbjct: 407 AITNNLPMGFLVSILFLILTTIFVATTGDSMSYVISATMTKG--DTPSTAVRVFWGIAMG 464

Query: 498 LVAIALML--GGGLAAAQAMAVTTGLPFTIVLL 528
           ++A+ L+    GG++  Q+  V T +P +++LL
Sbjct: 465 VMAVILISVGSGGVSKLQSFIVVTAVPVSLILL 497


Lambda     K      H
   0.327    0.141    0.435 

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: 807
Number of extensions: 40
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: 553
Length of database: 514
Length adjustment: 35
Effective length of query: 518
Effective length of database: 479
Effective search space:   248122
Effective search space used:   248122
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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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