GapMind for catabolism of small carbon sources

 

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

Align Altronate dehydratase (EC 4.2.1.7) (characterized)
to candidate WP_053935921.1 WG78_RS01020 altronate dehydratase

Query= reanno::Pedo557:CA265_RS19875
         (548 letters)



>NCBI__GCF_001294205.1:WP_053935921.1
          Length = 532

 Score =  553 bits (1425), Expect = e-162
 Identities = 280/545 (51%), Positives = 373/545 (68%), Gaps = 17/545 (3%)

Query: 5   ILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMYGVLV 64
           IL IHP+D++LVAL +LA G+ V ++G   ++   + AKHKF  +++  G+ + +YGV V
Sbjct: 4   ILCIHPDDDMLVALVDLAAGQLVSWEGDSILINTPVAAKHKFARRNLAQGELLKLYGVPV 63

Query: 65  GKAQHFILKGGLMDTENTKH-ASDPYEFRPYHYEWHAPDVSKFEGRTFNGYIRSDGRVGT 123
           G+A   I +G  + TEN +H A+D        Y+W APD+++++  TF G +R+DGRVGT
Sbjct: 64  GRAMAPIRRGEAVTTENLEHYAADVEIAATQPYQWTAPDMARWQDATFEGVVRADGRVGT 123

Query: 124 ANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEADPSS 183
           ANYWL  P VFCENRN++ +R AL   LGYA  D   +Y   L+     GE +A      
Sbjct: 124 ANYWLIFPLVFCENRNVEHLRNALEGPLGYATQD-LAAYTLALL-----GEEMA------ 171

Query: 184 IGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLSLGC 243
              A  +  R F NVDG++ + H GGCGGTR DA  L K+LAAYADHPNVAG+TV SLGC
Sbjct: 172 ---APRAVTRPFANVDGVRIITHAGGCGGTRADARSLCKVLAAYADHPNVAGITVFSLGC 228

Query: 244 QNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIERQPA 303
           QN Q+  F D LK R+P FDKP  ++EQQ+  SE+ ++K  ++ T  GL   N + RQP 
Sbjct: 229 QNAQISMFQDALKARNPAFDKPCLIYEQQKWDSEDAMMKAVLQDTLNGLKAANAVTRQPV 288

Query: 304 PLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLIDRTK 363
           PLS L +GVKCGGSDGFSG+SANPA+G  SD++VA+GG  +LAEFPELCG E  LI+R +
Sbjct: 289 PLSALKIGVKCGGSDGFSGLSANPAMGLVSDMVVAVGGGSILAEFPELCGVEASLIERCQ 348

Query: 364 DETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSPVED 423
           ++   R+F+ +M  +   A+ VG+ F  NPSPGNI+DGLITDAIKS GAAKKGGTSP+  
Sbjct: 349 NDDDKRRFLGMMRDFEARAQAVGTSFAANPSPGNIRDGLITDAIKSAGAAKKGGTSPIVS 408

Query: 424 VLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKVSTN 483
           VLDY EPA +PGL+L+CTPG DVE+ TG  ASGA ++LF+TGLGTPTGNP+ P +K++TN
Sbjct: 409 VLDYGEPAARPGLSLLCTPGGDVESVTGIVASGANVVLFSTGLGTPTGNPIVPVLKIATN 468

Query: 484 NALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFIPWK 543
             +  R+ D+ID +CGPVI G   + ++ E + E  ++ A G    KA  L Q DFI WK
Sbjct: 469 TRMATRLKDMIDFDCGPVISG-TPLPEVAEGLFEMVLQTAGGRYRAKADRLQQYDFIFWK 527

Query: 544 RGVSL 548
           R +SL
Sbjct: 528 RDISL 532


Lambda     K      H
   0.317    0.136    0.400 

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: 770
Number of extensions: 41
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: 548
Length of database: 532
Length adjustment: 35
Effective length of query: 513
Effective length of database: 497
Effective search space:   254961
Effective search space used:   254961
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: 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