GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Rhodobacter viridis JA737

Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_110805806.1 C8J30_RS10480 TRAP transporter substrate-binding protein

Query= reanno::SB2B:6938088
         (339 letters)



>NCBI__GCF_003217355.1:WP_110805806.1
          Length = 333

 Score =  254 bits (650), Expect = 2e-72
 Identities = 137/316 (43%), Positives = 193/316 (61%), Gaps = 1/316 (0%)

Query: 22  ATVLGFSFGAVAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPNSQLFG 81
           A  L  S  A+AEP+ IKFSHVVA +TPKG+ A KF+EL E    G   V V+PNSQL+ 
Sbjct: 15  ALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAAKFEELAEKYTNGAVDVEVYPNSQLYK 74

Query: 82  DNNELAALLLNDVQLVAPSLSKFERY-TKKLQVFDLPFLFEDMDAVDRFQQSEAGQQLLN 140
           D  EL AL L  VQ++APSL+KF     +  +VFDLP++F+D +A+ +  Q EAG+ LL+
Sbjct: 75  DKEELEALQLGAVQMLAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHKVTQGEAGKMLLS 134

Query: 141 SMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIPVKKP 200
            +  KG+ GL +  NG K  SAN+ L+ P D  G K RI  S V+ A+  A+GA+P    
Sbjct: 135 KLEAKGITGLAFWDNGFKIMSANSPLNTPDDFLGLKMRIQSSKVLEAEMNALGAVPQVMA 194

Query: 201 FSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKSLPKD 260
           FSEV+  LQT  +DG EN  SN++++K  EVQ H T SNHG L Y ++ ++ FW  LP D
Sbjct: 195 FSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYLGYAVIVNKQFWDGLPAD 254

Query: 261 KREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRPVWSQ 320
            R  ++++M E+    N +A E+  +    +  +   E   LT E+R AW  A+ PV  +
Sbjct: 255 VRTGLEKAMAESTDYANGIAREENEKALAAMKAAGTTEFHELTAEERAAWEEALAPVADE 314

Query: 321 FEDKIGKDLIEAAESA 336
             D+IG + I A ++A
Sbjct: 315 MADRIGAETIAAVKAA 330


Lambda     K      H
   0.316    0.132    0.368 

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: 261
Number of extensions: 10
Number of successful extensions: 2
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: 339
Length of database: 333
Length adjustment: 28
Effective length of query: 311
Effective length of database: 305
Effective search space:    94855
Effective search space used:    94855
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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