Alignments for a candidate for cadA in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Shewanella sp. ANA-3

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate 7026738 Shewana3_3871 ornithine decarboxylase (RefSeq)

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__ANA3:7026738
          Length = 720

 Score =  373 bits (957), Expect = e-107
 Identities = 230/643 (35%), Positives = 330/643 (51%), Gaps = 28/643 (4%)

Query: 118 LRGILYLFEDTVPFLARQVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAY 177
           + G+  L      F  +QV  A + Y   LLPPFF  L ++    N ++  PGH GG  +
Sbjct: 78  ITGVFELCGSNTDFYGKQVETAVQKYEQALLPPFFGTLKKYVEMGNSTFACPGHQGGQFF 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 SEFSKQSIAAKI-AASPLARGREPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFD 355
             F +  +  +I A +P     +   +LA++   TYDG  YNA  +   +G   + + FD
Sbjct: 258 HCFQESYLREQIRAVAPERADEQRPFRLAIIQLGTYDGTIYNARQVVDRIGHLCDYILFD 317

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

Query: 412 RKLDVARFNEAFMMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALAN 471
           R  +  RFN AFMMH STSP Y + A+LDV + M EG +GR L +E     +  R+ L  
Sbjct: 378 RYCNHKRFNNAFMMHASTSPFYPLFAALDVNAKMHEGASGRYLWREAVKAGIEARKLLL- 436

Query: 472 VRQNLDRNDWWFGVWQPEQVEG-------TDQVG--THDWVLEPSADWHGFGDIAEDYVL 522
                 +   +   + P  +EG       T+Q+      +  EP   WH F    +    
Sbjct: 437 ------KKCKYIKPFIPSMIEGRPWQDYPTEQMADDLRFFEFEPGQKWHSFDGYEKGQYF 490

Query: 523 LDPIKVTLTTPGLSA-GGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKG 581
           +DP K  LTTPG+ A  GK +E GIPA I++ FL E  ++ EK  L S L L +      
Sbjct: 491 VDPCKFLLTTPGIDAETGKYTEFGIPATILANFLRENNIIPEKCDLNSILFLMTPAEDMA 550

Query: 582 KWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAK 641
           K   LV+++  F++  D + PL +VLP+V  A   RY    +R L   MH  Y  +   +
Sbjct: 551 KMQHLVSQISRFEKLVDEDAPLSEVLPNVYNANKARYKDYTIRQLCQEMHNLYVSHDVKQ 610

Query: 642 AMKRMY--TVLPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPG 699
             K M+     P   M P EA  + +RG+VE VP++++EGRIAA   +PYPPG+  ++PG
Sbjct: 611 LQKEMFRQAHFPTKVMDPQEANLEFIRGKVELVPLSQIEGRIAAEGALPYPPGVLCVVPG 670

Query: 700 ERFTEATRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSGR 742
           E +  A +     LE         PGF  ++ G+  +  P G+
Sbjct: 671 EIWGGAVQRYFLALEEGINL---LPGFSPELQGVYLETPPDGK 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: 1143
Number of extensions: 65
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources