GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dino:3608018 Dshi_1425 aldehyde dehydrogenase
           (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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