Alignments for a candidate for Psest_0084 in Pseudomonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Pseudomonas stutzeri A1501

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate WP_011915052.1 PST_RS20150 DUF3394 domain-containing protein

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



>NCBI__GCF_000013785.1:WP_011915052.1
          Length = 850

 Score =  278 bits (712), Expect = 6e-79
 Identities = 214/715 (29%), Positives = 324/715 (45%), Gaps = 130/715 (18%)

Query: 21  VALLFSIYQIVTAA-------FHPVSSQVLRAGHVGFLLLLVFLCYPARGNGK----PFQ 69
           +ALL+S++Q+  A+       F  ++    R+ H+ F LLL FL YPA         P  
Sbjct: 32  LALLWSLFQLWIASPLPFILGFGVLNDTETRSIHLAFALLLAFLAYPAFKRSPRDRVPLM 91

Query: 70  PVAWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPI 129
            +A  LGL   A   Y +   + L QR G++TT D+V     I L+ EA RR +G  L I
Sbjct: 92  DIA--LGLVAAACAAYLFLAYSQLAQRPGNLTTLDLVTACVGIPLLLEATRRALGPPLAI 149

Query: 130 ICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGS 189
           I  +FL Y + G ++PG LAHRG     + N     TEG++G    VS +++FLF+LFG+
Sbjct: 150 IALVFLVYSVAGPWMPGLLAHRGVSFTALANHQWITTEGVFGIALGVSTSFVFLFVLFGA 209

Query: 190 FLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTT--------- 240
            LE+AG    F   A  + GH  GGPAK +VV+S + G I+GS +ANVVTT         
Sbjct: 210 LLERAGAGHYFIQLAFSMLGHFRGGPAKAAVVASGMTGLISGSSIANVVTTGTFTIPMMK 269

Query: 241 -------------------GQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAF 281
                              GQ   P+M    +      G+     +    +P ++  +A 
Sbjct: 270 RTGFSAEKAGAVEVASSVNGQIMPPVMGAAAFLMVEYVGIPYVEVIKHAFLPALISYIAL 329

Query: 282 IMAETIN--------VPFVEIAK------------AALIPAL---LYFG----------S 308
           I    +         +P   +AK            AALI  L   +Y+G          +
Sbjct: 330 IYIVHLESLKLGLQALPRANVAKPWMQRLIGFAFGAALISGLSLGVYYGLGWLKPALGDA 389

Query: 309 VFWMVH--LEAKRAGL--------------KGLPKDECPSAMAAVKERWYLLIPLVVLVW 352
             W++   L     GL                +P ++ P     +    + L+P+VVLVW
Sbjct: 390 ALWVIAGLLALVYLGLLKIAASNPPLPHEDPNMPLEKLPETRPVLLSGLHFLLPVVVLVW 449

Query: 353 LLFSGR-TPMFAGTIGLALTAIVILGSAIILKVSNFALRIAFWIALGLLCAGFFQLGIGV 411
            L   R +P  +   G  +  I++L    +L                     + +     
Sbjct: 450 CLMIERLSPGLSAFWGSVMLVIILLTQRPLLS--------------------WMRHDRSH 489

Query: 412 IFGVIAALVAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVSLTGVAS 471
           + G                D ++     L+ GAR+ + +GIA A  G+I+G VS TGV  
Sbjct: 490 VDGTFM-------------DGVIDLREGLIAGARNMIGIGIATAAAGIIVGAVSQTGVGL 536

Query: 472 TFAGYILAVGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLG------V 525
             A  +  +   NL L LLLT    L+LGMG+PT  NYI+ SS+ AP ++ LG      V
Sbjct: 537 VLADLVELLSMGNLLLMLLLTAFLSLILGMGLPTTANYIVVSSLLAPVIVALGQQNGLIV 596

Query: 526 PLIVSHMFVFYFGIMADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVY 585
           PLI  H+FVFYFGIMAD+TPPV LA FAAA ++K   ++  + A   ++    +PF+ ++
Sbjct: 597 PLIAVHLFVFYFGIMADVTPPVGLASFAAAAVSKGDPIRTGVTAFYYSLRTAALPFLFIF 656

Query: 586 NPALMMQGGDWGATLYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASM 640
           N  L++ G D+   + +   A  A+ ++ A   GY       +E +L    A ++
Sbjct: 657 NTDLLLIGVDFWHGVLIFIVATIAMLIFAAGTQGYFLVRSRWYESLLLLLVAFTL 711


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: 1640
Number of extensions: 95
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 2
Length of query: 674
Length of database: 850
Length adjustment: 40
Effective length of query: 634
Effective length of database: 810
Effective search space:   513540
Effective search space used:   513540
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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