Alignments for a candidate for Psest_0084 in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Marinobacter adhaerens HP15

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate GFF1092 HP15_1070 TRAP-type uncharacterized transport system, fused permease component

Query= reanno::psRCH2:GFF84
         (674 letters)



>FitnessBrowser__Marino:GFF1092
          Length = 867

 Score =  364 bits (935), Expect = e-105
 Identities = 230/694 (33%), Positives = 356/694 (51%), Gaps = 83/694 (11%)

Query: 18  LFYVALLFSIYQIVTAA-------FHPVSSQVLRAGHVGFLLLLVFLCYPA-RGNGKPFQ 69
           LF V L++S++Q+  A+       F   +S   R+ H+ F + L F  +P  +G      
Sbjct: 39  LFIVPLVWSLFQLWIASPLPYIFNFAIFNSTEARSIHLAFAVFLAFSAFPMIKGRHVNIV 98

Query: 70  PVA-WLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALP 128
           P+  W+L L       Y + F  +L  R G   T D+ V L  +VL+ EA RR +G+ L 
Sbjct: 99  PIYDWILALVAAFCASYLYVFYEELSTRPGAPITQDLWVALIGLVLLLEATRRSLGLPLT 158

Query: 129 IICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFG 188
           I+ A+F+ Y + G Y+P  +AH+G  L ++ +    GTEG++G    VS +++FLF+LFG
Sbjct: 159 IVAAVFITYSIAGPYMPDVIAHKGVSLSKLASHQWLGTEGVFGVALGVSTSFVFLFVLFG 218

Query: 189 SFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLM 248
           + LE+AG    F   A  + GH  GGPAK +VVSS L G I+GS +ANVVTTG FTIPLM
Sbjct: 219 ALLERAGAGNYFIKVAYAMLGHMRGGPAKAAVVSSGLSGVISGSSIANVVTTGTFTIPLM 278

Query: 249 KRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGS 308
           KR G+    AG VE  +S   Q+ PP+MGA AF+M E + + ++E+ K A++PA++ + +
Sbjct: 279 KRVGFPATKAGAVEVAASTNGQLTPPIMGAAAFLMVEYVGISYLEVIKHAILPAMISYVA 338

Query: 309 VFWMVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVL------------------ 350
           + ++VHLEA +  ++G+ +   P+    +     +LI L VL                  
Sbjct: 339 LIYIVHLEACKLNMQGIERLNKPTLAQRLLNWVVILIGLSVLTLAVYYGVGWTKTLFGEA 398

Query: 351 -VWLLFSGRTPMFAGTIGLAL-------------------------TAIVILGSAII--- 381
            +W+L      ++ G +G A                          T +  L   ++   
Sbjct: 399 AMWVLAPLLVLIYVGLVGYATRFPELEEDDPEKDMGELPPVGPTVKTGLYFLLPVVVLVW 458

Query: 382 -LKVSNFALRI-AFWIALGLLCAGFFQLGIGVIFGVIAALVAVCWFIKGG------RDTL 433
            L V  F+ ++ AFW  L +            IF V+       +F K G      +D +
Sbjct: 459 CLTVERFSPQLSAFWATLFM------------IFIVVTQRPLKAFFYKHGNFLGEFKDGV 506

Query: 434 VICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVASTFAGYILAVGENNLFLSLLLTM 493
               H+L  GAR+ V +G+A A  G+++G V+LTG+      ++  +   NL L L+ T 
Sbjct: 507 FDLAHSLATGARNMVGIGVATATAGIVVGTVTLTGIGLVMTEFVEFLSGGNLLLMLIFTA 566

Query: 494 LTCLVLGMGIPTIPNYIITSSIAAPALLDLG------VPLIVSHMFVFYFGIMADLTPPV 547
           +  L+LGMG+PT  NYI+ S++ AP ++ LG      VPLI  H+FVFYFGI+AD TPPV
Sbjct: 567 IISLILGMGLPTTANYIVVSTLMAPVIVTLGAQNGLIVPLIAVHLFVFYFGILADDTPPV 626

Query: 548 ALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQG-GDWGATLYMLFKA 606
            LA +AAA I+    ++  +      I   I+PFM ++N  L++ G   W   L  +F A
Sbjct: 627 GLAAYAAAAISGADPIRTGIQGFTYDIRTAILPFMFIFNTQLLLIGLTGWFDLLVTIFSA 686

Query: 607 AFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASM 640
             A+ ++ A   G+       WE +L      +M
Sbjct: 687 VTAMLVFSAATQGFWFTKSYKWESLLLLLITFTM 720


Lambda     K      H
   0.330    0.143    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: 1639
Number of extensions: 80
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 674
Length of database: 867
Length adjustment: 40
Effective length of query: 634
Effective length of database: 827
Effective search space:   524318
Effective search space used:   524318
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 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 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