GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Phaeo:GFF3740 PGA1_262p01440 BCCT transporter
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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