GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Marinobacter adhaerens HP15

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate GFF3754 HP15_3696 acyl-CoA dehydrogenase domain protein

Query= BRENDA::Q60759
         (438 letters)



>FitnessBrowser__Marino:GFF3754
          Length = 689

 Score = 74.7 bits (182), Expect = 8e-18
 Identities = 102/369 (27%), Positives = 151/369 (40%), Gaps = 62/369 (16%)

Query: 113 YGCAGVSSVAYGLLTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGE 172
           YG  G+ + + GLL +E+    +   SM    S   M+ I+ +G+E+Q+Q YL  L +G 
Sbjct: 183 YGGQGLPA-SMGLLKQEMMGTANWPFSMYPGLSLGAMNTIFLHGTEDQKQTYLAPLTEGR 241

Query: 173 LLGCFGLTEPNHGSDPGGMETRARHNPSNQSYTLSGTKTWITNSPVADL-----FIVWAR 227
             G   LTEP  G+D G ++T+A    ++ SY L+GTK +I++    DL      IV AR
Sbjct: 242 WAGTMCLTEPQCGTDLGQVKTKAEPQ-ADGSYRLTGTKIFISSGD-HDLTENIVHIVLAR 299

Query: 228 CED-----NCIRGFILEKGM----------RGLSAPRIEGKFSLRASATGMIIMDSVEVP 272
             D       I  FI+ K +           G+    +E K  ++ASAT ++  D     
Sbjct: 300 LPDAPKGTRGISLFIVPKFLPDSNGDVGERNGVVCGSLEKKMGIKASATCVLNFDG--AT 357

Query: 273 EENVLPNVSSLAGPFGCLNTARYGITWGVLGAAEFCLHTARQYALDR------------- 319
              + P    L   F  +NTAR G     +G AE     A  YA DR             
Sbjct: 358 GFLIGPENDGLNCMFTFMNTARIGTAIQGVGPAELSYQWALAYAKDRRSMRALSGKKEPD 417

Query: 320 -----IQFGVPLARNQLVQKKLAD-----MLTEITLGLHAC--LQLGRLKDQDK------ 361
                +     + R  L QK +A+     +     L  H       G  K  DK      
Sbjct: 418 QVADSLIHHADVRRMLLTQKAIAEGGRAMLYYAARLADHMVEGFTEGDEKKADKYDDKLG 477

Query: 362 -ATPEMVSMLKRNNCGKALDIARQARDILGGNGISDEYHVIRHAMNLEAVNTYEGTHDIH 420
             TP +   L    C    + A     + GG+G   E+ + +   +      YEGT  I 
Sbjct: 478 FLTPILKGFLTELGC----EAANLGVQVFGGHGYIREHGMEQIVRDTRIATLYEGTTGIQ 533

Query: 421 AL-ILGRAI 428
           AL +LGR +
Sbjct: 534 ALDLLGRKV 542


Lambda     K      H
   0.320    0.136    0.408 

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: 600
Number of extensions: 30
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 438
Length of database: 689
Length adjustment: 36
Effective length of query: 402
Effective length of database: 653
Effective search space:   262506
Effective search space used:   262506
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 (21.8 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