GapMind for catabolism of small carbon sources

 

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

Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate WP_053935921.1 WG78_RS01020 altronate dehydratase

Query= curated2:P42240
         (510 letters)



>NCBI__GCF_001294205.1:WP_053935921.1
          Length = 532

 Score =  189 bits (480), Expect = 2e-52
 Identities = 151/493 (30%), Positives = 233/493 (47%), Gaps = 47/493 (9%)

Query: 41  LVLEEDVPQGHKVALTDLNQGDEIVRYGEVIGFADETIKRGSWIREALVRMPAPPALDDL 100
           +++   V   HK A  +L QG+ +  YG  +G A   I+RG    EA+          D+
Sbjct: 33  ILINTPVAAKHKFARRNLAQGELLKLYGVPVGRAMAPIRRG----EAVTTENLEHYAADV 88

Query: 101 PLANRVPQP--RPPLEGY---TFEGYRNADGSAGTKNILGITTSVQC-----------VV 144
            +A   P     P +  +   TFEG   ADG  GT N   I   V C           + 
Sbjct: 89  EIAATQPYQWTAPDMARWQDATFEGVVRADGRVGTANYWLIFPLVFCENRNVEHLRNALE 148

Query: 145 GVLDYAVKRI---------KEELLPK-----YPNVDDVVPLHHQYGCGVAINAPDAVIPI 190
           G L YA + +         +E   P+     + NVD V  + H  GCG      DA    
Sbjct: 149 GPLGYATQDLAAYTLALLGEEMAAPRAVTRPFANVDGVRIITHAGGCGGT--RADARSLC 206

Query: 191 RTIQNLAKHPNFGGEVMVIGLGCEK----LLPERIASEN---DDDILSLQDHRGFA--AM 241
           + +   A HPN  G + V  LGC+     +  + + + N   D   L  +  +  +  AM
Sbjct: 207 KVLAAYADHPNVAG-ITVFSLGCQNAQISMFQDALKARNPAFDKPCLIYEQQKWDSEDAM 265

Query: 242 IQSILEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTANPAVGYAADLLVRAG 301
           ++++L+     L   N+ TR   P+S L IG++CGGSD FSG++ANPA+G  +D++V  G
Sbjct: 266 MKAVLQDTLNGLKAANAVTRQPVPLSALKIGVKCGGSDGFSGLSANPAMGLVSDMVVAVG 325

Query: 302 ATVLFSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGDADRSANPSPGNKKG 361
              + +E  E+      L  R  +++  +  +  M+ +++  +      +ANPSPGN + 
Sbjct: 326 GGSILAEFPELCGVEASLIERCQNDDDKRRFLGMMRDFEARAQAVGTSFAANPSPGNIRD 385

Query: 362 GLSNVVEKALGSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDFVCGTLQLAAGMNLQ 421
           GL     K+ G+  K GTSPI  VL  GE A + GL    TP  D    T  +A+G N+ 
Sbjct: 386 GLITDAIKSAGAAKKGGTSPIVSVLDYGEPAARPGLSLLCTPGGDVESVTGIVASGANVV 445

Query: 422 VFTTGRGTPYGLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEASIEDVGWEIFRTIL 481
           +F+TG GTP G    PVLK++T   ++    D+ID + G + +G   + +V   +F  +L
Sbjct: 446 LFSTGLGTPTGNPIVPVLKIATNTRMATRLKDMIDFDCGPVISG-TPLPEVAEGLFEMVL 504

Query: 482 DVASGRKQTWADR 494
             A GR +  ADR
Sbjct: 505 QTAGGRYRAKADR 517


Lambda     K      H
   0.318    0.136    0.406 

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: 667
Number of extensions: 35
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: 510
Length of database: 532
Length adjustment: 35
Effective length of query: 475
Effective length of database: 497
Effective search space:   236075
Effective search space used:   236075
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 (21.7 bits)
S2: 52 (24.6 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