GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Caulobacter crescentus NA1000

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate CCNA_02347 CCNA_02347 phosphomannomutase/phosphoglucomutase

Query= BRENDA::Q6I7B6
         (450 letters)



>FitnessBrowser__Caulo:CCNA_02347
          Length = 498

 Score =  142 bits (357), Expect = 3e-38
 Identities = 128/425 (30%), Positives = 194/425 (45%), Gaps = 30/425 (7%)

Query: 25  VGMAVGTY----KSGKALVGRDGRTSSVMLKNAMISGLLSTGMEVLDADLIPTPALAWGT 80
           +G+ +GTY       K +VG D R+ S  +KNA+I GL+S G EV D  L  +P   +  
Sbjct: 48  LGLGLGTYIHELGQSKIVVGHDFRSYSTSIKNALILGLISAGCEVHDIGLALSPTAYFAQ 107

Query: 81  RKLADAGV-MITASHNPPTDNGVKVFNGDGTEFYVEQERGLEEIIFSGNFRKARWDEIKP 139
             L    V M+TASHN     GVK+       F  ++   L+ I+ +  F +   D  K 
Sbjct: 108 FDLDIPCVAMVTASHNENGWTGVKMGAQKPLTFGPDEMSRLKAIVLNAEFVER--DGGKL 165

Query: 140 VRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLLREMG-AKVLSVNAHVDG 198
           +R       YI+ V         LKV+    NG         L++MG A+V+ ++  +D 
Sbjct: 166 IRVQGEAQRYIDDVAKRASVTRPLKVIAACGNGTAGAFVVEALQKMGVAEVVPMDTDLDF 225

Query: 199 HFPGRKPEPR-YENIAYLGKLVRELGVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFA 257
            FP   P P   E +  +   VRE G DLA   DGD DR  V D++G  +  D +  + A
Sbjct: 226 TFPKYNPNPEDAEMLHAMADAVRETGADLAFGFDGDGDRCGVVDDEGEEIFADKIGLMLA 285

Query: 258 KLYVEEHGGGTVVVSIDTGS--RIDAVVERAGGRVVRIPLGQPHDGIKRYKAIFAA---- 311
           +     H G T VV + +      D ++ + G +V+    G  H  IKR  A   A    
Sbjct: 286 RDLAPLHPGATFVVDVKSTGLYATDPILAQHGCKVIYWKTG--HSYIKRKSAELGALAGF 343

Query: 312 --EPWKLVHPKFGPWIDPFVTMGLLIKLIDENGP---LSELVKEIPTYYLKKA-NVLCPD 365
                  ++ + G   D  +T    I  + +  P   LS++ K +P  +     +  C D
Sbjct: 344 EKSGHFFMNGELGYGYDCGLTAAAAILAMLDRNPGVKLSDMRKALPVAFTSLTMSPHCGD 403

Query: 366 EYKAEVVRRAAEEVERK-------LSSEIKEVLTISGFRIALNDGSWILIRPSGTEPKIR 418
           E K  VV    +E E         L  +I EV+T++G R+ L DGSW+L+R S  +P++ 
Sbjct: 404 EVKYGVVADVVKEYEDLFAAGGSILGRKITEVITVNGVRVHLEDGSWVLVRASSNKPEVV 463

Query: 419 VVAEA 423
           VV E+
Sbjct: 464 VVVES 468


Lambda     K      H
   0.318    0.138    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: 563
Number of extensions: 37
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 450
Length of database: 498
Length adjustment: 33
Effective length of query: 417
Effective length of database: 465
Effective search space:   193905
Effective search space used:   193905
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: 51 (24.3 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