GapMind for catabolism of small carbon sources

 

Aligments for a candidate for uxaC in Azospirillum brasilense Sp245

Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate AZOBR_RS31425 AZOBR_RS31425 glucuronate isomerase

Query= curated2:Q1GNM2
         (470 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS31425 AZOBR_RS31425 glucuronate
           isomerase
          Length = 467

 Score =  639 bits (1649), Expect = 0.0
 Identities = 314/470 (66%), Positives = 370/470 (78%), Gaps = 10/470 (2%)

Query: 7   LSPDRLFPSDPAQRDIARRLYKAVAGLPIVSPHGHTDPAWFAGDAPFGNAAELLLHPDHY 66
           L PDRLFPSDP QRDIARRLY  V  LPI+SPHGHTDP+WFA +  F N A L + PDHY
Sbjct: 2   LHPDRLFPSDPTQRDIARRLYAEVGHLPIISPHGHTDPSWFAKNEAFPNPAALFVVPDHY 61

Query: 67  VFRMLYSQGVSLDALGI-----GNADADPRESWRLFAENYHLFRATPSRMWMDWVFAEVF 121
            FRMLYSQGV+L++LG+     G  ++DPR+ WR  A+N+HLFR TP+RMW+D  F  VF
Sbjct: 62  AFRMLYSQGVALESLGVPRTDGGAVESDPRKIWRQLAQNWHLFRGTPTRMWLDHAFETVF 121

Query: 122 GFDVQLSAETSDLYYDRITEALAIDAFRPRALFDRFGIEVIATTESPLDSLDHHAVIRAA 181
           G   +LS  ++D  +D+I   L    F PRALF+RF IE++ATTESPLD+L+HH  IR +
Sbjct: 122 GVTERLSGASADRIFDQIDACLQKPEFLPRALFERFNIELLATTESPLDTLEHHRAIRES 181

Query: 182 NASGEWGGRVITAYRPDPVVDPEFEGFRDNLARFSNLSGEDAFSYSGYLAAHRKRRAFFA 241
                W GRVITA+RPDPVVDPEFEGF+ N+ R   LSGE+  +++GYLAA R RR +F 
Sbjct: 182 G----WKGRVITAFRPDPVVDPEFEGFQANVERLGALSGENTGTWAGYLAALRNRRQYFK 237

Query: 242 SMG-ATSTDHGHPSAATADLSETQAEALFARVTGEDMSAADAELFRAHMLTVMAGMSLDD 300
            +G ATSTDHGH +A TADLS+  AE LF +     ++AA+AE+FR  MLT MA MSLDD
Sbjct: 238 EVGGATSTDHGHATATTADLSDADAERLFEKALRGTITAAEAEIFRGQMLTEMAKMSLDD 297

Query: 301 GLVMQIHPGAFRNHNPWLFANHGRDKGADIPTATDYVHALRPLLGRYGNEADLTIILFTL 360
           GLVMQIHPG+FRNHNP +F   GRDKGADIPT T+YV AL+PLL R GNE DLTIILFTL
Sbjct: 298 GLVMQIHPGSFRNHNPGVFERFGRDKGADIPTGTEYVRALKPLLDRVGNERDLTIILFTL 357

Query: 361 DETSYARELAPLAGHYPALKLGPAWWFHDSPEGMRRFRSQMTETAGFYNTVGFNDDTRAF 420
           DETSYARELAPLAGHYPAL++GPAWWFHDSPEGMRR+R  +TETAGFYNTVGFNDDTRAF
Sbjct: 358 DETSYARELAPLAGHYPALRVGPAWWFHDSPEGMRRYREMITETAGFYNTVGFNDDTRAF 417

Query: 421 LSIPARHDVARRIDCGFLAQLVSEHRLEEWEAAELAADLSYNLAKASYKL 470
            SIPARHDVARR+DC FLA+LV+EHRLEE EAAE+A DL+Y LAK +YKL
Sbjct: 418 CSIPARHDVARRVDCAFLARLVAEHRLEEDEAAEVAVDLAYTLAKKAYKL 467


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: 806
Number of extensions: 31
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: 470
Length of database: 467
Length adjustment: 33
Effective length of query: 437
Effective length of database: 434
Effective search space:   189658
Effective search space used:   189658
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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