GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Caulobacter crescentus NA1000

Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate CCNA_00436 CCNA_00436 acyl-CoA dehydrogenase, short-chain specific

Query= SwissProt::P81140
         (408 letters)



>FitnessBrowser__Caulo:CCNA_00436
          Length = 382

 Score =  148 bits (373), Expect = 3e-40
 Identities = 115/369 (31%), Positives = 172/369 (46%), Gaps = 16/369 (4%)

Query: 38  DTFRTYCQEHLMPRIVLANRNEVFHREIISEMGELGVLGPTI-KGYGCAGVSSVAYGLLA 96
           DT   +  E L P       N+    ++I EM  LG+ G TI + +G  G++     L+A
Sbjct: 13  DTVARFVAERLRPIEAQVAENDAVPDDVIEEMKGLGLFGLTIPEEFGGLGLTMEEEALVA 72

Query: 97  RELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGCFGLTEPNHGS 156
            EL R    +RS       +    +  +G++EQ+  K+LP +A G ++  F LTEP  GS
Sbjct: 73  IELGRASPAFRSVFGTNVGIGSQGLVMFGNDEQKA-KWLPGIASGAVITSFALTEPEAGS 131

Query: 157 DPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDNC-----IRGFLLEKG 211
           D  +++TRA  +  +  Y LNG+K +ITN+  A LF V AR   +      +  FL+ + 
Sbjct: 132 DSAAVQTRATRDGDD--YILNGSKRYITNAGKASLFTVMARTNPDAKGGAGVSAFLVPRD 189

Query: 212 MRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVL-PKASSLAVPFGCLNNARYGISWG 270
           + GL+  K E K   + +    +  D+V VP  N L  +     V    L+  R  I+  
Sbjct: 190 LPGLTVGKPEKKMGQQGAHIHDVTFDNVRVPAWNRLGAEGEGFKVAMQVLDRGRLHIAAV 249

Query: 271 VLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITLGLHACLQLGRLKDQD 330
            +G AE  +     Y  +R QFG P+A  QLIQ  +AD  TE        L+  R +D  
Sbjct: 250 CVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIADSKTEALAAKALVLETARKRDAG 309

Query: 331 -KVTPEMVS--LLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTH 387
             VT E  S  L      G+  D A Q   + GG G   +Y + R   ++     YEGT 
Sbjct: 310 VNVTLEAASSKLFASEMVGRVADRAVQ---VFGGAGYVADYGIERLYRDVRIFRIYEGTS 366

Query: 388 DIHALILGR 396
            +  LI+ R
Sbjct: 367 QVQQLIIAR 375


Lambda     K      H
   0.319    0.136    0.404 

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: 315
Number of extensions: 23
Number of successful extensions: 6
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: 408
Length of database: 382
Length adjustment: 31
Effective length of query: 377
Effective length of database: 351
Effective search space:   132327
Effective search space used:   132327
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: 50 (23.9 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