GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Pedobacter sp. GW460-11-11-14-LB5

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate CA265_RS18400 CA265_RS18400 iron-sulfur cluster-binding protein

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__Pedo557:CA265_RS18400
          Length = 461

 Score =  270 bits (691), Expect = 9e-77
 Identities = 156/422 (36%), Positives = 230/422 (54%), Gaps = 19/422 (4%)

Query: 53  EVADAKDHAAK-----NMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKK 107
           E +  K H  K     N+D    +F++  ++RG KV  A  A EA + I  I + NN K 
Sbjct: 46  EASKKKAHVIKWRVMENLDKFLPEFESNFQRRGGKVIWANDAEEAQQEILNIIKRNNGKT 105

Query: 108 AIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADL 167
            IKSKSMT EE HLN  LE++N+E +E+DLGE+I+Q+  + P H+V PA+HLS   +A L
Sbjct: 106 VIKSKSMTTEEIHLNDFLEKNNIESLESDLGEYIVQLLGQAPYHIVTPAMHLSATDIAQL 165

Query: 168 FSEVTKQKQEVDIQRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLV 227
           F +      +    +LV+ AR  LR  +  AD+GISG NF +A+TG+I L  NEGNARL 
Sbjct: 166 FHDKFGTPIDATPPQLVQKARELLRDKYLNADIGISGGNFLIADTGSIALTENEGNARLS 225

Query: 228 TTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRK 287
           TT P++H+A+ G++K++P++ D      +L  + TGQ +T Y T + G  +     DG +
Sbjct: 226 TTFPKIHIAIVGIEKVIPSIADLDLFWPLLASHGTGQNLTVYNTILSGPRQPNE-TDGPE 284

Query: 288 EMHIVFLDNGRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILT 347
           EM+++ LDNGR  L       Q L C+RCGAC N CPVY+ +GGH     Y G IG ++T
Sbjct: 285 EMYVILLDNGRTNLLAQKDQRQGLYCIRCGACLNACPVYKNIGGHTYNTTYSGPIGSVIT 344

Query: 348 YFFHGRDKARNLVQNCINCESCKHICAGGIDLPR--LIKEIRARLNEEEGMPVETTLMGK 405
               G ++ ++L      C  C  +C   ID+ +  L+    A    E G   E      
Sbjct: 345 PHLKGMEEFKHLSYASSLCGKCSEVCPVKIDIHKMLLLNRRDAAAGHENGKKEEI----- 399

Query: 406 MLKNRKLFHTLLRFAKWAQKPVTGGTPYIRHLPQIFAKDHG-FKALPAIADKPFRDEWET 464
                 +F  +++  KW      GG      L + F K  G ++ +P +ADK F  +WE 
Sbjct: 400 ---GWSMFSRMMQKRKWMD--FFGGKFKNFMLKRFFKKSWGKYREMPKVADKSFAKQWEE 454

Query: 465 VR 466
           ++
Sbjct: 455 MK 456


Lambda     K      H
   0.321    0.135    0.402 

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: 763
Number of extensions: 33
Number of successful extensions: 4
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: 717
Length of database: 461
Length adjustment: 36
Effective length of query: 681
Effective length of database: 425
Effective search space:   289425
Effective search space used:   289425
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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:

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. 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:

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:

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