Alignments for a candidate for cadA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Escherichia coli BW25113

Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate 17044 b2965 ornithine decarboxylase isozyme (VIMSS)

Query= BRENDA::Q9Z4R7
         (709 letters)



>FitnessBrowser__Keio:17044
          Length = 711

 Score =  354 bits (909), Expect = e-102
 Identities = 229/660 (34%), Positives = 337/660 (51%), Gaps = 54/660 (8%)

Query: 75  LPVFILKPTDCDKPVDFGAVGDHATFIDCHLFSNEDVVDKIEKAICHYIDNITPPFTKAL 134
           LPVF+      + P    AV          +  NE    ++E A C Y +N+ PPF   L
Sbjct: 58  LPVFLYSEHAVELPAGVTAV----------INGNEQQWLELESAACQYEENLLPPFYDTL 107

Query: 135 FDYVDKNKYTFCTPGHMSGTAFLKSPVGSLFYDFYGENTFKSDISVSMGELGSLLDHSGP 194
             YV+    TF  PGH  G  F K P G  FYDF+GEN F++D+  +  +LG LL H G 
Sbjct: 108 TQYVEMGNSTFACPGHQHGAFFKKHPAGRHFYDFFGENVFRADMCNADVKLGDLLIHEGS 167

Query: 195 HKEAEEYIAETFNADHSYIVTNGTSTANKIVGMYSVPAGSTVLIDRNCHKSLTH-LLMMS 253
            K+A+++ A+ F+AD +Y V NGTS ANK+V    +  G  VL DRN HKS  H  L+ +
Sbjct: 168 AKDAQKFAAKVFHADKTYFVLNGTSAANKVVTNALLTRGDLVLFDRNNHKSNHHGALIQA 227

Query: 254 DITPVYLKPTRNAYGILGGIPQKEFTKEVITEKLTKVPGATWPVH-----AVITNSTYDG 308
             TPVYL+ +RN +G +GGI    F +E + +++  V      +      A+I   TYDG
Sbjct: 228 GATPVYLEASRNPFGFIGGIDAHCFNEEYLRQQIRDVAPEKADLPRPYRLAIIQLGTYDG 287

Query: 309 LFYNTDKIKDTLD--VKSIHFDSAWVPYTNFSPIYNGKTGMGGK-QVKDKVIFETHSTHK 365
             YN  ++ DT+      I FDSAWV Y  F P+    + +  +    D  IF T S HK
Sbjct: 288 TVYNARQVIDTVGHLCDYILFDSAWVGYEQFIPMMADSSPLLLELNENDPGIFVTQSVHK 347

Query: 366 LLAAFSQASMIHVKGN--LNTATF------GEAYMMHTSTSPFYPMVASTEVAAAMMRGN 417
             A FSQ S IH K N     A F        A+M+H STSPFYP+ A+ +V A +  G 
Sbjct: 348 QQAGFSQTSQIHKKDNHIRGQARFCPHKRLNNAFMLHASTSPFYPLFAALDVNAKIHEGE 407

Query: 418 SGKRLMQDSLERAVKFRKEIKKHKAHADSWYFDVWQPENVDNIECWELHQTD-------- 469
           SG+RL  + +E  ++ RK I      A    F  + P  VD  + W+ + T         
Sbjct: 408 SGRRLWAECVEIGIEARKAIL-----ARCKLFRPFIPPVVDG-KLWQDYPTSVLASDRRF 461

Query: 470 -------KWHGFKDIDAQHMYLDPIKVTLLTPGLD-KNGELEKTGIPANLVSKFLEDRGI 521
                  KWHGF+   A   ++DP K+ L TPG+D + GE    G+PA +++ +L + GI
Sbjct: 462 FSFEPGAKWHGFEGYAADQYFVDPCKLLLTTPGIDAETGEYSDFGVPATILAHYLRENGI 521

Query: 522 IVEKTGPYNILVLFSIGVDDTKALSLLHALNEFKSLYDANATVEEVLPRVFNESPSFYQE 581
           + EK    +IL L +      K   L+  L +F+   + ++ + EVLP V+N+ P  Y++
Sbjct: 522 VPEKCDLNSILFLLTPAESHEKLAQLVAMLAQFEQHIEDDSPLVEVLPSVYNKYPVRYRD 581

Query: 582 MRIQELAQGIHSLICKHNLPELMFSAF--EVLPTMVMNPHKAFQLELKGQIEDCYLEDMV 639
             +++L Q +H L    ++ +L  + F  +  P++VMNP  A    ++G +E   + D  
Sbjct: 582 YTLRQLCQEMHDLYVSFDVKDLQKAMFRQQSFPSVVMNPQDAHSAYIRGDVELVRIRDAE 641

Query: 640 GKINANMILPYPPGVPLVMPGEMITEESKPILEFLMMLCEIGAHFPGFETDIHGAYRQED 699
           G+I A   LPYPPGV  V+PGE+       +  + + L E     PGF  ++ G Y + D
Sbjct: 642 GRIAAEGALPYPPGVLCVVPGEV---WGGAVQRYFLALEEGVNLLPGFSPELQGVYSETD 698


Lambda     K      H
   0.319    0.137    0.412 

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: 1311
Number of extensions: 71
Number of successful extensions: 10
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: 709
Length of database: 711
Length adjustment: 39
Effective length of query: 670
Effective length of database: 672
Effective search space:   450240
Effective search space used:   450240
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:

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