Alignments for a candidate for cadA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Shewanella amazonensis SB2B

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate 6939240 Sama_3334 ornithine decarboxylase (RefSeq)

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__SB2B:6939240
          Length = 720

 Score =  363 bits (933), Expect = e-104
 Identities = 233/661 (35%), Positives = 332/661 (50%), Gaps = 19/661 (2%)

Query: 93  LPIFALGEQVTIENAPAESMADLHQLRGILYLFEDTVPFLARQVARAARNYLAGLLPPFF 152
           LPIF     V  E A  +   D   + G+  L      F  +QV  A R Y   LLPPFF
Sbjct: 58  LPIFV---SVCCEEAFPDDFCDT--ITGVFELCNAKTDFYGKQVETAVRRYQESLLPPFF 112

Query: 153 RALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAFHQFFGENTLRSDLSVSVPELGSLLDH 212
             L ++    N ++  PGH GG  +RK PVG+ F  FFGE   RSD+  +  +LG LL H
Sbjct: 113 GTLKKYVEMGNSTFACPGHQGGQFFRKHPVGRQFFDFFGETVFRSDMCNADVKLGDLLIH 172

Query: 213 TGPLAEAEDRAARNFGADHTFFVINGTSTANKIVWHSMVGREDLVLVDRNCHKSILH-SI 271
            G   +A+  AA+ + AD T+FV+NGTS +NK+V ++++   DLVL DRN HKS  H ++
Sbjct: 173 EGAPHDAQAYAAKVYNADKTYFVLNGTSASNKVVCNALLAPGDLVLFDRNNHKSNHHGAL 232

Query: 272 IMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAAKIAASPLARGREPK-VKLAVVTNST 330
           I  GA P+YL   RN  G IG I    F +  +  +I      R +  +  +LA++   T
Sbjct: 233 IQAGATPVYLETARNPFGFIGGIDSHCFDEAYLRDEIGKVAPERVQAARPFRLAIIQLGT 292

Query: 331 YDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHEFYDGRYGMGTSRSEEGPLVFATHS 390
           YDG  YNA  +   +G   + + FD AW  Y  F         +      E P +  T S
Sbjct: 293 YDGTIYNARQVVDRIGHLCDYILFDSAWVGYEQFIPMMKDCSPLLLELGAEDPGIIVTQS 352

Query: 391 THKMLAAFSQASMIHVQD----GGTRKLDVARFNEAFMMHISTSPQYGIIASLDVASAMM 446
            HK  A FSQ S IH +D    G  R  +  RFN AFMMH STSP Y + A+LDV + M 
Sbjct: 353 VHKQQAGFSQTSQIHKKDSHIKGQERYCNHKRFNNAFMMHASTSPFYPLFAALDVNAKMH 412

Query: 447 EGPAGRSLIQETFDEALSFRRALANVRQNLDRNDWWFGVWQPEQVEGTDQVG--THDWVL 504
           EG +GR L +E     +  R+ L    + +          +P Q   T+++      +  
Sbjct: 413 EGASGRYLWREAVKAGIEARKLLLKKCKYIKPFIPTTVEGEPWQSFDTERMADDLRFFEF 472

Query: 505 EPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSA-GGKLSEQGIPAAIVSRFLWERGLVVE 563
           EP   WH F    +    +DP K  LTTPG++A  G+  + GIPA I++ FL E  ++ E
Sbjct: 473 EPGLKWHAFDGYEKGQYFVDPCKFLLTTPGINAETGEYEDFGIPATILANFLRENNIIPE 532

Query: 564 KTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGL 623
           K  L S L L +      K   LVT++  F++  D + PL +VLP+V +   +RY G  +
Sbjct: 533 KCDLNSILFLMTPAEDMAKMQHLVTQIARFEKLIDEDAPLSEVLPNVYRTNRERYEGYSI 592

Query: 624 RDLSDAMHASYRDNATAKAMKRMYTV--LPEVAMRPSEAYDKLVRGEVEAVPIARLEGRI 681
           R L   MH  Y      +  K M+     P+  M P +A    VRG+ E VP++ +EG+I
Sbjct: 593 RRLCQEMHDLYVSRNVKQLQKEMFRAAHFPKAVMNPQDANIAFVRGKAELVPLSEIEGQI 652

Query: 682 AAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFERAFPGFDSDVHGLQHQDGPSG 741
           AA   +PYPPG+  ++PGE +  A +     LE         PGF  ++ G+  +   +G
Sbjct: 653 AAEGALPYPPGVLCMVPGEVWGGAVQRYFLALEEGINL---LPGFAPELQGVYLERADNG 709

Query: 742 R 742
           R
Sbjct: 710 R 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: 1172
Number of extensions: 62
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