Alignments for a candidate for fadB in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Algoriphagus machipongonensis PR1

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

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000166275.1:WP_008197813.1
          Length = 800

 Score =  716 bits (1848), Expect = 0.0
 Identities = 373/800 (46%), Positives = 524/800 (65%), Gaps = 11/800 (1%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M + I+  A+LGSGVMGS IA H ANIG+ VLLLDIVP +LT++E+KKGLTK+   VR+R
Sbjct: 1   MKRTIKNVAILGSGVMGSRIACHFANIGVQVLLLDIVPFELTEQEQKKGLTKEDPAVRNR 60

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           L   A++  LK  P+ +        I  GN +DD  K+K+ DW++EVVVE L++K+ +F 
Sbjct: 61  LVNSALQSTLKSNPSAIYDKAFADRIQTGNFDDDLHKIKDYDWVMEVVVERLDIKQSLFE 120

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            V++HRK G++++SNTSGI +  M EGRS+DF+ +F GTHFFNP RYL+LLEIIP  ++ 
Sbjct: 121 KVEKHRKPGTLITSNTSGIPMHMMCEGRSEDFQENFAGTHFFNPPRYLRLLEIIPGPKSK 180

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
           P+ ++F+  +G+  LGK  V  KDTP FIANR+G Y ++  +  + K G  V EVD +TG
Sbjct: 181 PENIEFLMDYGDRFLGKETVLCKDTPAFIANRVGVYAIISAMHTVEKMGLGVSEVDKMTG 240

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299
            +IGR KSATFRT+DVVGLDT  +VA N+Y     DE +E F++P  +  + E  W G K
Sbjct: 241 TVIGRAKSATFRTMDVVGLDTTVNVANNLYKALPNDESREKFKLPKIVEVLYENKWFGDK 300

Query: 300 AGQGFYK----KEG-KTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354
            G G++K    K+G K + E+D  T  Y +  K    AL+A+K+ +  K ++K L+  DD
Sbjct: 301 TGHGYFKMIRHKDGSKELKEIDFETFEYKDVEKPNIKALQASKEIEDLKKRIKFLVNFDD 360

Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414
           +AG            Y +  + EI+D+++ IDQA+  GFGWELGPFE WD +G+K++ EK
Sbjct: 361 KAGEFYRTTFYDLFKYCSNRIPEISDELYRIDQAVCAGFGWELGPFETWDVLGVKETVEK 420

Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETK 472
           +E  G     W+ EML+ GN++FY    G   YYD     Y+ +   ++ I L  LK   
Sbjct: 421 MEAAGEKPAAWVYEMLEAGNDSFYQVIEGKKHYYDIPTKSYKEIPGIEEFIILDTLKSAG 480

Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532
             + +N GAS+ D+GDDV  LEFH+K N++G ++I+ I+  +   E+++KGLVIGN+G N
Sbjct: 481 KKLWENPGASVYDMGDDVIGLEFHTKMNSMGQEVIEGINTAIGMAEKSHKGLVIGNEGAN 540

Query: 533 FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACL 592
           F  GANLAM+ M   D +F E++ +I +FQ TMM+ ++S+ PVV AP  M LGGG E  L
Sbjct: 541 FSAGANLAMLFMFAGDQDFDEINLMIAQFQNTMMRARFSSIPVVLAPHNMALGGGCELSL 600

Query: 593 PAARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMA 649
            +  IQA +E YMGLVE GVGLIP GGG KE+   + N +  G   +N   + F  IAMA
Sbjct: 601 HSDHIQAHAELYMGLVEVGVGLIPAGGGTKEMTLRFSNEIESGDVELNRLQERFMNIAMA 660

Query: 650 KVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGY 709
           KVS SA+EAR +  L+ +D I++N+   L +AKQ   SLYD G+  PV++ +KV G++  
Sbjct: 661 KVSTSAEEARNLGYLRNSDGITLNRKRQLAEAKQKVISLYDQGYSQPVEQNIKVMGKSSL 720

Query: 710 AALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSG 769
           A    G   M+   YISEHD KIA+KLA+V++GG +   TEV E +LL++EREAFLSL+G
Sbjct: 721 ALFEAGITGMQYGAYISEHDAKIARKLAWVMSGGDLSSPTEVSERHLLDLEREAFLSLTG 780

Query: 770 EAKSQARMQHMLVKGKPLRN 789
           E K+  R+  +L KGKPLRN
Sbjct: 781 EKKTLERIHSILFKGKPLRN 800


Lambda     K      H
   0.316    0.134    0.382 

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: 1522
Number of extensions: 80
Number of successful extensions: 6
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: 789
Length of database: 800
Length adjustment: 41
Effective length of query: 748
Effective length of database: 759
Effective search space:   567732
Effective search space used:   567732
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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