GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Shewanella amazonensis SB2B

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__SB2B:6938545
          Length = 498

 Score =  281 bits (720), Expect = 3e-80
 Identities = 176/485 (36%), Positives = 264/485 (54%), Gaps = 34/485 (7%)

Query: 4   KLLINGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTP 60
           +  ING      G++     +P  G +L ++A       D AV  A A F    W   +P
Sbjct: 22  RAFINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGVWSLQSP 81

Query: 61  KVRAECLLKLADVIEENGQVFAELESRNCGKPL-HSAFNDEIPAIVDVFRFFAGAARCLN 119
             R + +++ A+++E +    A LE+ + GKP+ HS         VDV    AGAAR + 
Sbjct: 82  VKRKKVMIRFAELLEAHADELALLETLDMGKPIAHSK-------AVDV----AGAARAIR 130

Query: 120 GLAAGEYLE-----------GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNC 168
              +GE ++               MI R+P+GVVA+I PWN+P++MA WKL PALA GN 
Sbjct: 131 W--SGEAIDKIYDELAPTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNS 188

Query: 169 VVLKPSEITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIA 227
           VVLKPSE +PLTA+++A+LAK+   P GV+N+L G G TVG  L  H  V  +  TGS  
Sbjct: 189 VVLKPSEKSPLTAIRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTK 248

Query: 228 TGEHIISHTA-SSIKRTHMELGGKAPVIVFDDA-DIEAVVEGVRTFGYYNAGQDCTAACR 285
             + ++ +   S++KR  +E GGK+P IVF+DA D++A  E   +   +N G+ CTA  R
Sbjct: 249 IAKQLMVYAGQSNMKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSR 308

Query: 286 IYAQKGIYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIK 345
           +  + G+ D L++ +   +   + G P D +T  G +     L+ V   ++     G  K
Sbjct: 309 LLVESGVKDELIKLIVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEG-AK 367

Query: 346 VITGGEK--RKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQ 403
           ++ GG +   +  G Y APT+  G      I ++E+FGPV+SV  FD  ++ V  AND+ 
Sbjct: 368 LMCGGSQVLAETGGVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTI 427

Query: 404 YGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLED 463
           YGLA+ VWT D+ +AH+ +  L+ G  W+N +       P GG K SG G+D SL+  E 
Sbjct: 428 YGLAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEK 487

Query: 464 YTVVR 468
           YT V+
Sbjct: 488 YTEVK 492


Lambda     K      H
   0.317    0.134    0.397 

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: 582
Number of extensions: 29
Number of successful extensions: 6
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: 474
Length of database: 498
Length adjustment: 34
Effective length of query: 440
Effective length of database: 464
Effective search space:   204160
Effective search space used:   204160
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