GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaC in Caulobacter crescentus NA1000

Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate CCNA_01557 CCNA_01557 uronate isomerase

Query= curated2:Q1GNM2
         (470 letters)



>FitnessBrowser__Caulo:CCNA_01557
          Length = 487

 Score =  627 bits (1618), Expect = 0.0
 Identities = 313/474 (66%), Positives = 365/474 (77%), Gaps = 8/474 (1%)

Query: 1   MPRPLYLSPDRLFPSDPAQRDIARRLYKAVAGLPIVSPHGHTDPAWFAGDAPFGNAAELL 60
           M RPL    DRLFPSDPA R  AR LY  V  LPI+SPHGHTDP+WFA +APF +A +LL
Sbjct: 1   MARPLSFHEDRLFPSDPATRSYARGLYALVKDLPIISPHGHTDPSWFATNAPFQDATDLL 60

Query: 61  LHPDHYVFRMLYSQGVSLDALGI----GNADADPRESWRLFAENYHLFRATPSRMWMDWV 116
           L PDHY+FRMLYSQGVSLDAL +    G  D DPRE+WR+FA +++LFR TPS +W++ V
Sbjct: 61  LAPDHYLFRMLYSQGVSLDALKVRSKAGVPDTDPREAWRVFASHFYLFRGTPSWVWLNHV 120

Query: 117 FAEVFGFDVQLSAETSDLYYDRITEALAIDAFRPRALFDRFGIEVIATTESPLDSLDHHA 176
           F++VFGF   L A  +D Y+DRIT ALA DAFRPRALFDRF IE +ATTE P +SL HHA
Sbjct: 121 FSQVFGFTEFLEASNADDYFDRITAALATDAFRPRALFDRFNIETLATTEGPHESLQHHA 180

Query: 177 VIRAANASGEWGGRVITAYRPDPVVDPEFEGFRDNLARFSNLSGEDAFSYSGYLAAHRKR 236
            IR +     WGG VITAYRPD V+D E E       RF+  SG+D +S+  YL AHR R
Sbjct: 181 AIRESG----WGGHVITAYRPDAVIDFEDERSPRAFERFAETSGQDVYSWKSYLEAHRLR 236

Query: 237 RAFFASMGATSTDHGHPSAATADLSETQAEALFARVTGEDMSAADAELFRAHMLTVMAGM 296
           R  F   GATS+DHGHP+AATADLS+ +AEALF  +   D++   AELFRA MLT MA M
Sbjct: 237 RQAFIDAGATSSDHGHPTAATADLSDVEAEALFNSLVKGDVTPEKAELFRAQMLTEMAKM 296

Query: 297 SLDDGLVMQIHPGAFRNHNPWLFANHGRDKGADIPTATDYVHALRPLLGRYGNEADLTII 356
           SLDDGLVMQIHPG+ RNHN  L  +HGRDKGADIP  T+YV AL+PLL R GN+  L+II
Sbjct: 297 SLDDGLVMQIHPGSHRNHNVGLLNSHGRDKGADIPMRTEYVDALKPLLTRLGNDPRLSII 356

Query: 357 LFTLDETSYARELAPLAGHYPALKLGPAWWFHDSPEGMRRFRSQMTETAGFYNTVGFNDD 416
           LFTLDET+Y+RELAPLAGHYP LKLGP+WWFHDSPEGM RFR Q+TETAGFYNTVGFNDD
Sbjct: 357 LFTLDETTYSRELAPLAGHYPVLKLGPSWWFHDSPEGMMRFREQVTETAGFYNTVGFNDD 416

Query: 417 TRAFLSIPARHDVARRIDCGFLAQLVSEHRLEEWEAAELAADLSYNLAKASYKL 470
           TRAFLSIPARHDVARR+D  FLA++V+EHR++  EA EL  DL+YNL K +YKL
Sbjct: 417 TRAFLSIPARHDVARRVDSAFLARMVAEHRMDLVEAEELIVDLTYNLPKKAYKL 470


Lambda     K      H
   0.322    0.136    0.423 

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: 831
Number of extensions: 36
Number of successful extensions: 4
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: 470
Length of database: 487
Length adjustment: 34
Effective length of query: 436
Effective length of database: 453
Effective search space:   197508
Effective search space used:   197508
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 (21.9 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