Alignments for a candidate for Psest_0084 in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Pseudomonas stutzeri RCH2

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate GFF196 Psest_0197 TRAP transporter, 4TM/12TM fusion protein

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



>FitnessBrowser__psRCH2:GFF196
          Length = 850

 Score =  339 bits (869), Expect = 4e-97
 Identities = 246/695 (35%), Positives = 355/695 (51%), Gaps = 90/695 (12%)

Query: 21  VALLFSIYQIVTAA-------FHPVSSQVLRAGHVGFLLLLVFLCYPA--RGNGKPFQPV 71
           +ALL+S++Q+  A+       F  ++    R+ H+ F LLL FL YPA  R        V
Sbjct: 32  LALLWSLFQLWIASPLPFVLGFGVLNDTETRSIHLAFALLLAFLAYPAFKRSPRDRVPLV 91

Query: 72  AWLLGLAGFATFFYQWYFEADLIQRSGDMTTADMVVGLTLIVLVFEAARRVMGIALPIIC 131
              LGL   A+  Y +   + L QR G++TT D+V     I L+ EA RR +G  L II 
Sbjct: 92  DIALGLVAAASAAYLFIAYSQLAQRPGNLTTMDLVTACIGIPLLLEATRRALGPPLAIIA 151

Query: 132 ALFLAYGLLGEYLPGDLAHRGYYLDQIVNQLSFGTEGLYGTPTYVSATYIFLFILFGSFL 191
            +FL Y + G ++PG LAHRG     + N     TEG++G    VS +++FLF+LFG+ L
Sbjct: 152 LVFLVYSVAGPWMPGLLAHRGVSFTALANHQWITTEGVFGIALGVSTSFVFLFVLFGALL 211

Query: 192 EQAGMIKLFTDFAMGLFGHKLGGPAKVSVVSSALMGTITGSGVANVVTTGQFTIPLMKRF 251
           E+AG    F   A  + GH  GGPAK +VV+S + G I+GS +ANVVTTG FTIP+MKR 
Sbjct: 212 ERAGAGHYFIQLAFSMLGHFRGGPAKAAVVASGMTGLISGSSIANVVTTGTFTIPMMKRT 271

Query: 252 GYRPAFAGGVEATSSMGSQIMPPVMGAVAFIMAETINVPFVEIAKAALIPALLYFGSVFW 311
           G+    AG VE  SS+  QIMPPVMGA AF+M E + +P+VE+ K A +PAL+ + ++ +
Sbjct: 272 GFSAEKAGAVEVASSVNGQIMPPVMGAAAFLMVEYVGIPYVEVIKHAFLPALISYIALIY 331

Query: 312 MVHLEAKRAGLKGLPKDECPSAMAAVKERWYLLIPLVVLVWLLFSGRT-----------P 360
           +VHLE+ + GL+ LP+       A V + W   +   V    L SG +           P
Sbjct: 332 IVHLESMKLGLQALPR-------ANVAKPWMQRLIGFVFGAALISGLSLGVYYGLGWLKP 384

Query: 361 MFAGT----IGLALTAIVILGSAIILKVS-----------NFALRIAFWIALGLLCAGFF 405
           +   +    IG AL A+V LG   +LK++           N  L         LL    F
Sbjct: 385 LLGDSALWVIG-ALLAVVYLG---LLKIAASNPPLPHEDPNMPLEKLPETRPVLLSGLHF 440

Query: 406 QLGIGVIFGV-----IAALVAVCWFIKGGRDTLVICL---HALVEGARH-------AVPV 450
            L + V+        ++  ++  W    G   LVI L     L+   RH           
Sbjct: 441 LLPVVVLVWCLMIERLSPGLSAFW----GSVMLVIILLTQRPLLSWMRHDRSHPDGTFMD 496

Query: 451 GIACALVGVIIGVVSLTG--------------VASTFAGYILA-----VGENNLFLSLLL 491
           G+     G+I G  ++ G              V+ T  G +LA     +   NL L LLL
Sbjct: 497 GVIDLREGLIAGARNMIGIGIATAAAGIIVGAVSQTGVGLVLADLVELLSMGNLLLMLLL 556

Query: 492 TMLTCLVLGMGIPTIPNYIITSSIAAPALLDLG------VPLIVSHMFVFYFGIMADLTP 545
           T    L+LGMG+PT  NYI+ SS+ AP ++ LG      VPLI  H+FVFYFGIMAD+TP
Sbjct: 557 TAFLSLILGMGLPTTANYIVVSSLLAPVIVALGQQNGLIVPLIAVHLFVFYFGIMADVTP 616

Query: 546 PVALACFAAAPIAKERGLKISMWAIRIAIAGFIVPFMAVYNPALMMQGGDWGATLYMLFK 605
           PV LA FAAA ++K   ++  + A   ++    +PF+ ++N  L++ G D+   + +   
Sbjct: 617 PVGLASFAAAAVSKGDPIRTGVTAFYYSLRTAALPFLFIFNTDLLLIGVDFWHGVLIFIV 676

Query: 606 AAFAVGLWGAVFTGYLQRPMALWEKVLAFAAAASM 640
           A  A+ ++ A   GY       +E VL    A ++
Sbjct: 677 ATIAMLVFAAGTQGYFLVRSRWYESVLLLLVAFTL 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: 1615
Number of extensions: 90
Number of successful extensions: 4
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: 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 17 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