GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaC in Amantichitinum ursilacus IGB-41

Align Uronate isomerase; Glucuronate isomerase; Uronic isomerase; EC 5.3.1.12 (characterized)
to candidate WP_053935920.1 WG78_RS01015 glucuronate isomerase

Query= SwissProt::O34808
         (473 letters)



>NCBI__GCF_001294205.1:WP_053935920.1
          Length = 464

 Score =  450 bits (1158), Expect = e-131
 Identities = 216/465 (46%), Positives = 305/465 (65%), Gaps = 4/465 (0%)

Query: 1   MEPFMGKNFLLKNETAVSLYHNYAKDMPIIDYHCHLSPKEIYENKTFQNITEAWLYGDHY 60
           M  FM ++FLL +  A  LYH  A D+PIIDYH HL   EI   K F+NI E WL GDHY
Sbjct: 1   MTAFMDEDFLLDSHVAKRLYHEVAADLPIIDYHSHLQQGEIASRKQFRNIAELWLGGDHY 60

Query: 61  KWRIMRANGIEETYITGDAPDEEKFMAWAKTVPMAIGNPLYNWTHLELQRFFGIYEILNE 120
           KWR+MR+ G+ E +ITG+  DEEKF A+ K +P+AIGNP+Y+W+HLEL+R FGI  ++NE
Sbjct: 61  KWRLMRSAGVSEDFITGNRTDEEKFRAFCKVLPLAIGNPIYHWSHLELRRIFGIDLLINE 120

Query: 121 KSGSAIWKQTNKLLKGEGFGARDLIVKSNVKVVCTTDDPVDSLEYHLLLKEDKDFPVSVL 180
           K+ + IW++ N  L G    A   + ++ V+V CTTDDP D L  H  +K+  D    VL
Sbjct: 121 KNAAQIWERANARLAGMDTWA--FLEQAGVEVACTTDDPADDLAQHAAIKQ-MDLKTRVL 177

Query: 181 PGFRPDKGLEINREGFPEWVQALEDAAAISITTYDEFLKALEKRVRFFHSAGGRVSDHAI 240
           P +RPDK + IN++ F E++Q L   A + I ++ + ++AL +RV FF   G R+SDHA+
Sbjct: 178 PAYRPDKAMRINQQDFVEYLQRLGAVADVQIASFADMMQALAQRVTFFDEQGARISDHAV 237

Query: 241 DTMV-FAETTKEEAGRIFSDRLQGTEVSCEDEKKFKTYTLQFLCGLYAELDWAMQFHINA 299
           D  +       E+  ++F  RL GT +   +  ++    L  L  +YA  DW M  HI A
Sbjct: 238 DVALPVTPLPPEQIEQLFQKRLGGTLLEAAEVAQYVLAVLTGLGRVYAAHDWTMCLHIGA 297

Query: 300 LRNTNTKMMKRLGPDTGYDSMNDEEIAKPLYKLLNSVEMKNQLPKTILYSLNPNDNYVIA 359
            RN N +M+ RLG DTGYDS++D   +  L  LL++++ + +LPKT+L+ LNP  N +++
Sbjct: 298 QRNNNRRMLARLGADTGYDSISDMSCSAGLAGLLDTLDSEARLPKTMLFCLNPGMNEILS 357

Query: 360 SMINSFQDGITPGKIQFGTAWWFNDTKDGMLDQMKALSNVGLFSRFIGMLTDSRSFLSYT 419
           ++I +FQDG   GK+Q+G AWWFND K+G L Q+  L+N G+    +GM+TDSRSF SY 
Sbjct: 358 TLIGNFQDGSVAGKVQYGPAWWFNDHKEGNLQQLITLANHGVLGTSVGMVTDSRSFASYP 417

Query: 420 RHEYFRRIVCNLIGEWVENGEVPRDMELLGSIVQGICYDNAKHYF 464
           RH+YFRR++C  +G+WV  GE P D E L ++V+GICY+NAK YF
Sbjct: 418 RHDYFRRLLCRQLGQWVAGGEFPDDFEALSTVVRGICYENAKRYF 462


Lambda     K      H
   0.320    0.137    0.418 

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: 540
Number of extensions: 22
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: 473
Length of database: 464
Length adjustment: 33
Effective length of query: 440
Effective length of database: 431
Effective search space:   189640
Effective search space used:   189640
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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