GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Dinoroseobacter shibae DFL-12

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-15108
         (486 letters)



>FitnessBrowser__Dino:3608018
          Length = 484

 Score =  285 bits (730), Expect = 2e-81
 Identities = 170/469 (36%), Positives = 253/469 (53%), Gaps = 13/469 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           H I+G  V S    +F+  NPAT+E +         +++ A+ AAK A  G W  ++ +E
Sbjct: 21  HAINGALVDSAG--SFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPG-WAALSQDE 77

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R A +    D +   K+EL  L + + GKP     + ++  A +     +   R + +E 
Sbjct: 78  RGAYIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAIFWVREVAK--RRLEDEV 135

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
            +            P+GV+G I PWN P+LL  WK+AP L  GNT+VMKP+  TP+    
Sbjct: 136 IEDTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLR 195

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
             EI +    P GV+N+V G   N  GA LTEHPD+  ISFTG T TG+ +MAS++  LK
Sbjct: 196 FGEIAQQV-FPAGVLNVVAG--GNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLK 252

Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312
           R++ ELGG +P ++   ++   +I T   +++ N G+ C+   R+YV    Y+ FL  FV
Sbjct: 253 RITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFV 312

Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFL 372
           A   E  VG+  D  T +G + +   Y ++         +G ++  GG+ P+G   G F+
Sbjct: 313 AHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDG--PGNFV 370

Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432
             TI+    +D RVV+EE FGP++ +I +   +EV+   NDT +GL+ASVW  D   A  
Sbjct: 371 PITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIG 430

Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTN 481
           VA ++EAG VWVN   +  +  PFGG KQSG+G E G    E   E TN
Sbjct: 431 VANRLEAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQ---EGLKEFTN 476


Lambda     K      H
   0.318    0.136    0.404 

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: 581
Number of extensions: 31
Number of successful extensions: 5
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: 486
Length of database: 484
Length adjustment: 34
Effective length of query: 452
Effective length of database: 450
Effective search space:   203400
Effective search space used:   203400
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 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