GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cadA in Shewanella oneidensis MR-1

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate 199509 SO0314 ornithine decarboxylase, inducible (NCBI ptt file)

Query= SwissProt::Q9I2S7
         (751 letters)



>lcl|FitnessBrowser__MR1:199509 SO0314 ornithine decarboxylase,
           inducible (NCBI ptt file)
          Length = 720

 Score =  365 bits (938), Expect = e-105
 Identities = 229/644 (35%), Positives = 325/644 (50%), Gaps = 30/644 (4%)

Query: 118 LRGILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAY 177
           + G+  L      F  +QV  A + Y   LLPPFF  L ++    N ++  PGH GG  +
Sbjct: 78  ITGVFELCGSNTDFYGKQVETAIKKYEQALLPPFFGTLKKYVEMGNSTFACPGHQGGQFF 137

Query: 178 RKSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVIN 237
           RK PVG+ F  FFGE   RSD+  +  +LG LL H G   +A+  AA+ F AD T+FV+N
Sbjct: 138 RKHPVGRQFFDFFGETIFRSDMCNADVKLGDLLIHEGAPLDAQKYAAKVFNADKTYFVLN 197

Query: 238 GTSTANKIVWHSMVGREDLVLVDRNCHKSILH-SIIMTGAIPLYLTPERNELGIIGPIPL 296
           GTS++NK+  ++++ + DLVL DRN HKS  H ++I  GA P+YL   RN  G IG I  
Sbjct: 198 GTSSSNKVATNALLAKGDLVLFDRNNHKSNHHGALIQAGATPIYLETARNPFGFIGGIDA 257

Query: 297 SEFSKQSIAAKIAASPLARGREPK-VKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFD 355
             F +  +  +I      R  E +  +LA++   TYDG  YNA  +   +G   + + FD
Sbjct: 258 HCFKEAYLREQIREVAPERADEKRPFRLAIIQLGTYDGTIYNARQVVDRIGHLCDYILFD 317

Query: 356 EAWYAYAAFHEFYDGRYGMGTSRSEEGPLVFATHSTHKMLAAFSQASMIHVQD----GGT 411
            AW  Y  F    +    +    + E P +  T S HK  A FSQ S IH +D    G  
Sbjct: 318 SAWVGYEQFIPMMNDCSPLLLELTPEDPGIIVTQSVHKQQAGFSQTSQIHKKDKHIKGQA 377

Query: 412 RKLDVARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALAN 471
           R  +  RFN AFMMH STS  Y + A+LDV + M EG +GR L +E     +  R+ L  
Sbjct: 378 RYCNHKRFNNAFMMHASTSHFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLLK 437

Query: 472 --------VRQNLDRNDWWFGVWQPEQVEGTDQVG--THDWVLEPSADWHGFGDIAEDYV 521
                   +   +D   W        Q   T+Q+      +  EP   WH F    +   
Sbjct: 438 KCKYIKPFIPSMIDGRQW--------QDYPTEQMADDLRFFEFEPGQKWHSFEGYEKGQY 489

Query: 522 LLDPIKVTLTTPGLSA-GGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITK 580
            +DP K  LTTPG+ A  GK +E GIPA I++ FL E  ++ EK  L S L L +     
Sbjct: 490 FVDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDM 549

Query: 581 GKWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATA 640
            K   LV+++  F++  D + PL +VLP+V  A   RY    +R L   MH  Y  +   
Sbjct: 550 AKMQHLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMHNLYVSHDVK 609

Query: 641 KAMKRMY--TVLPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMP 698
           +  K M+     P   M P EA  + +RG VE VP++++EGRIAA   +PYPPG+  ++P
Sbjct: 610 QLQKEMFRHAHFPTKVMDPQEANLEFIRGNVELVPLSQIEGRIAAEGALPYPPGVLCMVP 669

Query: 699 GERFTEATRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSGR 742
           GE +  A +     LE         PGF  ++ G+  +  P G+
Sbjct: 670 GEIWGGAVQRYFLALEEGINL---LPGFSPELQGVYLESTPDGK 710


Lambda     K      H
   0.320    0.136    0.407 

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: 1141
Number of extensions: 66
Number of successful extensions: 7
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: 751
Length of database: 720
Length adjustment: 40
Effective length of query: 711
Effective length of database: 680
Effective search space:   483480
Effective search space used:   483480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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