GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Herbaspirillum seropedicae SmR1

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate HSERO_RS14035 HSERO_RS14035 C4-dicarboxylate ABC transporter

Query= SwissProt::A3QCW5
         (336 letters)



>FitnessBrowser__HerbieS:HSERO_RS14035
          Length = 344

 Score =  241 bits (615), Expect = 2e-68
 Identities = 128/305 (41%), Positives = 188/305 (61%), Gaps = 1/305 (0%)

Query: 33  PTEIKFSHVVAENTPKGQMALKFKQLVEERLPGEYQVNVFPNSQLFGDNNELSALLLNDV 92
           P  IKFSHVVA +TPKG+ A +FK+L E+   G  +V V+PNS L+ D  EL AL L  V
Sbjct: 33  PIIIKFSHVVANDTPKGKGAERFKELAEKATQGRVKVEVYPNSTLYKDKEELEALQLGSV 92

Query: 93  QFVAPSLSKFERY-TKKLQLFDLPFLFKDMDAVNRFQQSDAGQQLLNSMKRKGVVGLGYL 151
           Q +APSL+KF     ++ ++FDLP++F D   + R  +   GQ L   ++ KG+ GL Y 
Sbjct: 93  QMLAPSLAKFGPLGAREFEVFDLPYIFPDKAVLKRVTEGPIGQGLFQKLEGKGIKGLAYW 152

Query: 152 HNGMKQFSASSPLVLPEDAQGKKFRIMASDVLAAQFQAVEAIPVKKPFSEVFTLLQTRAI 211
            NGMK  +A+ PL    D +  K RI +S VL  QF+A++A P    FSEV+  +QT  +
Sbjct: 153 DNGMKVMTANRPLHKVADFRALKMRIQSSKVLDEQFRALKANPQVLAFSEVYQAMQTGVV 212

Query: 212 DGQENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSNTFWKSLPADKRKVIKASLDEAI 271
           DG ENT SN+Y++K +EVQSN+T S+HG + Y V+ +  FW++LPAD R  ++A++ +A 
Sbjct: 213 DGSENTPSNVYTQKMHEVQSNLTVSDHGYIGYAVIVNKKFWEALPADIRSQLEAAMKQAT 272

Query: 272 AYGNEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWVNAMKPVWAQFEDKIGKDLIDAA 331
            Y N IA  + +    AI  S ++ V  L+ +++A W  A+ PV      ++G DLI+A 
Sbjct: 273 LYANTIAQKENDDALAAIKASGKTRVYTLSEQEKAEWRRALLPVHKSMAARVGADLIEAI 332

Query: 332 VASNE 336
              +E
Sbjct: 333 YKESE 337


Lambda     K      H
   0.317    0.130    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: 269
Number of extensions: 15
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: 336
Length of database: 344
Length adjustment: 28
Effective length of query: 308
Effective length of database: 316
Effective search space:    97328
Effective search space used:    97328
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 (21.7 bits)
S2: 49 (23.5 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