Alignments for a candidate for ectP in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for ectP in Dinoroseobacter shibae DFL-12

Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate 3608081 Dshi_1486 BCCT transporter (RefSeq)

Query= SwissProt::Q87PP5
         (562 letters)



>FitnessBrowser__Dino:3608081
          Length = 621

 Score =  162 bits (410), Expect = 4e-44
 Identities = 99/304 (32%), Positives = 168/304 (55%), Gaps = 21/304 (6%)

Query: 72  ISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLLFAVGLLFSPL- 130
           I+  L+V  LI   +  P  A   L  + + I+  F+ +++++  FF++    L   P  
Sbjct: 29  ITGKLLVGGLILWAIAFPDQAASVLGALNSIILATFNIWYVYTMAFFVILCFALALWPTA 88

Query: 131 GKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGTPL-NAEAYSA 189
           GK+RLG  +  P+ S  SW SM+F AG+GIG+L ++ AEP  +F     T + + E  +A
Sbjct: 89  GKLRLGHDDDRPEFSNFSWFSMMFGAGIGIGMLTFATAEPMYHFGANPATIMGDTEGSTA 148

Query: 190 DAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYPIFGDRAWGWLGH 249
                A   +  HWG+  W+ YA+V LAL +F + +GLPL++R+A  PIFG++  G +GH
Sbjct: 149 GNVRDAYIWSFTHWGLAAWASYAIVGLALGYFCYRRGLPLTIRSALTPIFGNKLSGPVGH 208

Query: 250 VIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNGGIGTQ-------------MVVIA 296
           V+DI+AV++T+ G++ +LG G +Q  +G++ + G+   + T              +V + 
Sbjct: 209 VVDIVAVVATVLGVSQTLGFGVEQFIAGLSRI-GVGDWLYTATADGGQTSSTMGIIVALC 267

Query: 297 FVTFIAVLSVVRGIDGGVKLLSNVNMIVAFALLIFI-----TFITFDTAMGSLVDTTMAY 351
            +  ++ LS + G+  G+K LSN+NM ++F +LIF      TF    T    + D  ++ 
Sbjct: 268 VIMGLSTLSALSGVGKGIKWLSNLNMGLSFFVLIFFLIFGSTFFGLQTLFVGMFDYLVSI 327

Query: 352 IQNI 355
             NI
Sbjct: 328 PGNI 331



 Score =  139 bits (349), Expect = 4e-37
 Identities = 69/190 (36%), Positives = 115/190 (60%), Gaps = 8/190 (4%)

Query: 369 WMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLFAVIVIPTLVTLVWMSVFGGIAL 428
           W   WT+FYWAWW++++PFVG+F+AR+SKGRTVRE++   ++IP ++  VW ++ GG A+
Sbjct: 407 WQGAWTIFYWAWWIAFAPFVGVFLARISKGRTVREYVLGAMIIPAIMCFVWFALVGGTAI 466

Query: 429 DQVVNKV--GELGANGLTDISLTLFHVYDVLPYSSVISILSIVLILVFFITSSDSGSLVI 486
           D  +  V  G +   G  D    +  V      +  +S+L ++L+L + +TS+DS  L+I
Sbjct: 467 DLELRGVADGAIQGAGQADQLFAMLAVMLSEGLAYAMSVLIVILLLTYLVTSADSAVLII 526

Query: 487 DSITAGGKIDAPV--PQRIFWACIEGSIAAVMLWVGGKEALQALQSGVVATGLPFTFVLL 544
           ++I A G  + P   P  +FW      +   ++  GG   L A+Q+ +V   LPF+ V++
Sbjct: 527 NTINAAGD-EGPKARPHILFWGAALALVVGGLIIAGG---LGAIQTAMVIGALPFSVVMV 582

Query: 545 LMCVSLVKGL 554
           LM +SL+K +
Sbjct: 583 LMGLSLIKAV 592



 Score = 30.4 bits (67), Expect = 2e-04
 Identities = 43/180 (23%), Positives = 66/180 (36%), Gaps = 45/180 (25%)

Query: 81  LISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLLFAVGLLFSPLGKIRLGGKEA 140
           +++L ++  ++   AL+G+  GI       ++ + N  L F V + F   G         
Sbjct: 263 IVALCVIMGLSTLSALSGVGKGIK------WLSNLNMGLSFFVLIFFLIFG--------- 307

Query: 141 TPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGTPLNAEAYSADAKSLAMG--- 197
               ST   L  LF     +G+  + V+ P   FT W G P  A   S  A   A+    
Sbjct: 308 ----STFFGLQTLF-----VGMFDYLVSIPGNIFTVWVGAPAEAIIASVPASVQALPAED 358

Query: 198 -ATMFHWGVHGWSIYALVALALAFFAFNKGLPLS--------LRAAFYPIFGDRAWGWLG 248
            A M       W   A         +F +GLP S        + A +     +R  GW G
Sbjct: 359 LAAMVESATSPWGTLA---------SFTEGLPASAAALPAADIAAVYAAATENRLSGWQG 409


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: 999
Number of extensions: 72
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 562
Length of database: 621
Length adjustment: 37
Effective length of query: 525
Effective length of database: 584
Effective search space:   306600
Effective search space used:   306600
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 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:

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