Alignments for a candidate for cadA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Sinorhizobium meliloti 1021

Align Lysine decarboxylase LdcA; EC 4.1.1.18 (characterized)
to candidate SMa0680 SMa0680 amino acid (ornithine, lysine, arginine) decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__Smeli:SMa0680
          Length = 782

 Score =  432 bits (1110), Expect = e-125
 Identities = 262/701 (37%), Positives = 388/701 (55%), Gaps = 48/701 (6%)

Query: 76  LQDVVELIRVARVRAPQLPIFALGEQVTIENAPAESMADLHQLRGILYLFEDTVPFLARQ 135
           L+D  + +R  R    + P++AL +   I +  A  MA   ++ G +YL + T  F A+Q
Sbjct: 69  LEDARKFVRAVRDIGFRTPLWALADSHGIADIAAIKMAG--EVDGFVYLGQQTPAFYAKQ 126

Query: 136 VARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAFHQFFGENTL 195
           +  +  NY   LLPPFF  L+ +  ++N ++  PGH GG  YRKSP GQ F  +FGE+  
Sbjct: 127 IISSLVNYGKTLLPPFFGGLMAYDGEANIAFDCPGHQGGQFYRKSPAGQLFFNYFGESIF 186

Query: 196 RSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKIVWHSMVGRED 255
           R+DL  +  +LG LL H GP AEA+  AAR FGAD T+F++NGTST+NK+V ++++   D
Sbjct: 187 RADLCNADVDLGDLLIHEGPAAEAQKNAARIFGADRTYFILNGTSTSNKVVTNAVLRAGD 246

Query: 256 LVLVDRNCHKSILH--SIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAAKIAASPL 313
           LVL DRN HKS LH  +++  GAIP+YL   RN  G+IG +    + + S+  +I   PL
Sbjct: 247 LVLFDRNNHKS-LHQGALVQAGAIPVYLPTSRNSFGMIGAVDWDAWDEASLRRQIERHPL 305

Query: 314 ARGR-----EPKVKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHEFY 368
              +     E   +LA +  +TYDG  YN   + + +G   + + +DEAW  Y AFH  +
Sbjct: 306 VEDKARASAERPFRLACIQLATYDGTIYNVRKVLEQIGHLCDYVLWDEAWIGYNAFHPLF 365

Query: 369 DGRYGMGTSRSE-EGPLVFATHSTHKMLAAFSQASMIHVQD----GGTRKLDVARFNEAF 423
           +    M     + E P +F+T S HK  A FSQAS IH +D       R ++  RFNE+ 
Sbjct: 366 EDHSPMRIDTLDAEMPGLFSTQSVHKQGAGFSQASQIHKRDEHIRDQRRYVEHKRFNESL 425

Query: 424 MMHISTSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLD------ 477
           +MH+STSP Y + ASLDV + + EG AG  L     +  +  R+ L    +  +      
Sbjct: 426 LMHVSTSPFYPLFASLDVNAKIHEGKAGEMLWDRCIELGIEARKKLREFTRYYESSGAGP 485

Query: 478 RNDWWFGVWQPEQVEGTDQVGTHD--------------------WVLEPSADWHGFGDIA 517
           +  W+F  + P+ V  +    T D                    W   P A WHG+   +
Sbjct: 486 QEQWFFDPFVPDVVTISGSKHTEDVVESRWEALPTEVIKREQQCWRFRPGASWHGYSGYS 545

Query: 518 EDYVLLDPIKVTLTTPGLS-AGGKLSEQGIPAAIVSRFLWERGLVVEKTGLYSFLVLFSM 576
           + Y ++DP K+TL TPG+  A G+  + GIPA +V+ +L E+ +V EK  L S L L + 
Sbjct: 546 DGYAMVDPNKLTLLTPGIDRATGEYRDFGIPATMVANYLREQRIVPEKCDLNSILFLLTP 605

Query: 577 GITKGKWSTLVTELLEFKRCYDANLPLLDVLPSVAQAGGKRYNGVGLRDLSDAMHASYRD 636
              + K +TL+ +L++FK  +D + PL +VLP+V  A  +RY G  LR +   MH  YR 
Sbjct: 606 AEDESKLNTLIAKLVKFKNLWDRDAPLAEVLPTVFAANRERYAGYTLRQVCAEMHDFYR- 664

Query: 637 NATAKAMKRM---YTVLPEVAMRPSEAYDKLVRGEVEAVPIARLEGRIAAVMLVPYPPGI 693
            A  K ++R+      +PE AM P  AY+ LV  EV+ V +    GRI+A + + YPPGI
Sbjct: 665 QAGVKELQRLCFRAESMPEPAMTPKAAYEALVANEVDYVALDEAFGRISATLALIYPPGI 724

Query: 694 PLIMPGERFTEATRSILDY-LEFARTFERAFPGFDSDVHGL 733
            +I+PGER+ E  R + +Y L F  +F R FPGF+ +V G+
Sbjct: 725 GVIVPGERWDERARPMHNYFLAFQESFNR-FPGFNYEVQGV 764


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: 1390
Number of extensions: 68
Number of successful extensions: 8
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: 782
Length adjustment: 41
Effective length of query: 710
Effective length of database: 741
Effective search space:   526110
Effective search space used:   526110
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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Protein sequences (fasta format)
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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