Alignments for a candidate for fadB in Arenimonas metalli CF5-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Arenimonas metalli CF5-1

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_034211124.1 N787_RS04780 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000747155.1:WP_034211124.1
          Length = 789

 Score =  869 bits (2246), Expect = 0.0
 Identities = 460/809 (56%), Positives = 569/809 (70%), Gaps = 22/809 (2%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           M    ++KVAVLGAGVMGAQIAAHL+NA V  +LFDLPAKEGP NGI  +AI NL KLSP
Sbjct: 1   MPQLRIRKVAVLGAGVMGAQIAAHLVNADVDTILFDLPAKEGPPNGIVDKAIANLGKLSP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           AP   K +A  I  ANY+  + LLK+CDL+IEAIAERMDWK  LY ++  ++A +AI A+
Sbjct: 61  APFASKAKAAAITPANYDQHLDLLKDCDLIIEAIAERMDWKKALYDRIEAYVAPNAILAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSI  L++     L SRFCGVHFFNPPRYMHL ELIP A T  Q+L+ LE FL TT
Sbjct: 121 NTSGLSINDLAEVLPESLHSRFCGVHFFNPPRYMHLAELIPCAKTDKQVLEGLETFLVTT 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVV AKDTPNFI NR+G+FSIL+      +FG+ FD VD LTG  LGR KSAT+RT+
Sbjct: 181 LGKGVVYAKDTPNFIGNRIGVFSILSTLHHTAQFGLGFDEVDALTGPLLGRPKSATYRTS 240

Query: 241 DVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIK 300
           DVVGLDTMAHVIKTM DTL DDP+   +K P  LK L+D GALGQKTGAG + K+GK I 
Sbjct: 241 DVVGLDTMAHVIKTMADTLPDDPWHKYFKAPDWLKALIDKGALGQKTGAGIFMKKGKDIV 300

Query: 301 VLDAKTGQYVDA-GKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAV 359
           VLD K   Y  A G+ A E+V  +  K+ AE+   LR S +PQAQFLW+VFRD+FHY A 
Sbjct: 301 VLDLKAQDYRPATGEAAPEVVAILKNKNPAEKFAQLRASPHPQAQFLWSVFRDLFHYSAY 360

Query: 360 YLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAW 419
           +L  IA +A D+DLAIRWG+GW+ GPFE WQ+AGWKQVAEW+ ED+ AGK++S APLP W
Sbjct: 361 HLASIAETARDVDLAIRWGYGWSLGPFESWQAAGWKQVAEWIAEDIVAGKSMSNAPLPNW 420

Query: 420 VFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVE 479
           VF+G     +GVHAA GS+SP     + RS L VY RQ F   + G   ADP   G TV 
Sbjct: 421 VFDG----REGVHAAEGSFSPVRGEVLPRSNLSVYHRQRFPDPVLG-ERADP---GTTVF 472

Query: 480 ENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQL 539
           E D+VR+W     D + V+SFK+KMNT+G  V+ G+  AID AE  ++GLV+WQ      
Sbjct: 473 ETDSVRMW--HDGDGIAVLSFKTKMNTVGDGVLAGIGEAIDRAEKDFRGLVLWQTKE--- 527

Query: 540 GAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGG 599
                PFSAGA+L  AM +   G     E  VK FQ    R+KY+ VPV++A  G+ALGG
Sbjct: 528 -----PFSAGADLSGAMASLQAGRVDEFEAMVKTFQATSQRIKYSLVPVIAAVRGLALGG 582

Query: 600 GCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTS 659
           GCE  +HSA  V +LE+Y+GLVE GVGL+PAGGGLKE A+ A+ AA   G  ++   L  
Sbjct: 583 GCEFQMHSARSVFSLESYVGLVEAGVGLLPAGGGLKEIAVRASAAAGPGG--DVFAALKP 640

Query: 660 RFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT-L 718
            F++ AM KVSASALEA+++   + +D +VFN +ELL+VA+ +  ALA +GYR PLP   
Sbjct: 641 YFETVAMGKVSASALEAKELKLARDNDVVVFNQYELLHVAKAQALALAESGYRPPLPARQ 700

Query: 719 VPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALE 778
           V VAG  GIAT K  LVNM +G FIS HD+ ++SRIA  +CGG+V+ G++V E+WLL LE
Sbjct: 701 VQVAGDVGIATFKMMLVNMLEGRFISPHDYEVSSRIATVLCGGEVDRGAVVDEEWLLKLE 760

Query: 779 RKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           R+ FV L    KTQERI+  L+TGKP+RN
Sbjct: 761 REHFVALAQMPKTQERILHTLKTGKPLRN 789


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: 1554
Number of extensions: 61
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: 807
Length of database: 789
Length adjustment: 41
Effective length of query: 766
Effective length of database: 748
Effective search space:   572968
Effective search space used:   572968
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 2024 update 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