Alignments for a candidate for ech in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Algoriphagus machipongonensis PR1

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_008197813.1 ALPR1_RS01095 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000166275.1:WP_008197813.1
          Length = 800

 Score =  493 bits (1268), Expect = e-143
 Identities = 314/830 (37%), Positives = 456/830 (54%), Gaps = 62/830 (7%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLP-------------AKEGP--KNGIALR 50
           +K VA+LG+GVMG++IA H  N  V V+L D+               KE P  +N +   
Sbjct: 5   IKNVAILGSGVMGSRIACHFANIGVQVLLLDIVPFELTEQEQKKGLTKEDPAVRNRLVNS 64

Query: 51  AIENLKKLSPAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAP 110
           A+++  K +P+ +  K  A  IQ  N++DD+  +K+ D V+E + ER+D K  L++KV  
Sbjct: 65  ALQSTLKSNPSAIYDKAFADRIQTGNFDDDLHKIKDYDWVMEVVVERLDIKQSLFEKVEK 124

Query: 111 HLASHAIFATNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQIL 170
           H     +  +NTSG+ +  + +G   D +  F G HFFNPPRY+ L+E+IP   ++P+ +
Sbjct: 125 HRKPGTLITSNTSGIPMHMMCEGRSEDFQENFAGTHFFNPPRYLRLLEIIPGPKSKPENI 184

Query: 171 DQLEAFLTTTLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLG 230
           + L  +    LGK  V  KDTP FIANRVG+++I++     EK G+    VD +TG+ +G
Sbjct: 185 EFLMDYGDRFLGKETVLCKDTPAFIANRVGVYAIISAMHTVEKMGLGVSEVDKMTGTVIG 244

Query: 231 RAKSATFRTADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAG 290
           RAKSATFRT DVVGLDT  +V   +   L +D     +K P +++ L +    G KTG G
Sbjct: 245 RAKSATFRTMDVVGLDTTVNVANNLYKALPNDESREKFKLPKIVEVLYENKWFGDKTGHG 304

Query: 291 FYK----KEG-KAIKVLDAKTGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQ 344
           ++K    K+G K +K +D +T +Y D  K   + +    + +D  +RIK L    +   +
Sbjct: 305 YFKMIRHKDGSKELKEIDFETFEYKDVEKPNIKALQASKEIEDLKKRIKFLVNFDDKAGE 364

Query: 345 FLWAVFRDVFHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKED 404
           F    F D+F Y +  + +I+     ID A+  GFGW  GPFE W   G       VKE 
Sbjct: 365 FYRTTFYDLFKYCSNRIPEISDELYRIDQAVCAGFGWELGPFETWDVLG-------VKET 417

Query: 405 VEAGKALSAAPLPAWVFEGPVAEN----QGVHAAAGSWSPATQSFVARSKLPVYQRQAFR 460
           VE  +A    P  AWV+E   A N    Q +      +   T+S+    ++P  +     
Sbjct: 418 VEKMEAAGEKP-AAWVYEMLEAGNDSFYQVIEGKKHYYDIPTKSY---KEIPGIEEFIIL 473

Query: 461 AAIKGTAAADPRKAGRTVEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAID 520
             +K         AG+ + EN    ++  +  DDV+ + F +KMN++G +VI+G+  AI 
Sbjct: 474 DTLK--------SAGKKLWENPGASVY--DMGDDVIGLEFHTKMNSMGQEVIEGINTAIG 523

Query: 521 LAEAGYKGLVVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAKG---IEPFVKRFQDG 577
           +AE  +KGLV+        G  G  FSAGANL      FM  G +    I   + +FQ+ 
Sbjct: 524 MAEKSHKGLVI--------GNEGANFSAGANLAM---LFMFAGDQDFDEINLMIAQFQNT 572

Query: 578 MMRVKYASVPVVSAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEA 637
           MMR +++S+PVV A   +ALGGGCEL LHS    A  E Y+GLVEVGVGL+PAGGG KE 
Sbjct: 573 MMRARFSSIPVVLAPHNMALGGGCELSLHSDHIQAHAELYMGLVEVGVGLIPAGGGTKEM 632

Query: 638 ALAAARAAQAAGSTNILQFLTSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLY 697
            L  +   ++      L  L  RF + AMAKVS SA EAR +GYL+ SD I  N    L 
Sbjct: 633 TLRFSNEIESGDVE--LNRLQERFMNIAMAKVSTSAEEARNLGYLRNSDGITLNRKRQLA 690

Query: 698 VAQNEVRALASAGYRAPLPTLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEA 757
            A+ +V +L   GY  P+   + V G+S +A  +A +  M+ G +IS HD  IA ++A  
Sbjct: 691 EAKQKVISLYDQGYSQPVEQNIKVMGKSSLALFEAGITGMQYGAYISEHDAKIARKLAWV 750

Query: 758 VCGGDVEAGSLVSEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           + GGD+ + + VSE  LL LER+AF+ L G  KT ERI  +L  GKP+RN
Sbjct: 751 MSGGDLSSPTEVSERHLLDLEREAFLSLTGEKKTLERIHSILFKGKPLRN 800


Lambda     K      H
   0.319    0.134    0.391 

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: 1314
Number of extensions: 59
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: 807
Length of database: 800
Length adjustment: 41
Effective length of query: 766
Effective length of database: 759
Effective search space:   581394
Effective search space used:   581394
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 24 2021. The underlying query database was built on Sep 17 2021.

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

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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