GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Amantichitinum ursilacus IGB-41

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_053936559.1 WG78_RS04405 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_001294205.1:WP_053936559.1
          Length = 790

 Score =  913 bits (2360), Expect = 0.0
 Identities = 472/804 (58%), Positives = 586/804 (72%), Gaps = 22/804 (2%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPAPLGI 65
           +++VAVLGAGVMGAQIAAHL+NA +  VLFDLPAKEG  NGI  +A++NLKK+ PAP   
Sbjct: 7   IRRVAVLGAGVMGAQIAAHLVNAGIDTVLFDLPAKEGDANGIVKKAVDNLKKMKPAPFSS 66

Query: 66  KEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATNTSGL 125
              A  I  ANY  D+  L +CDL+IEAIAER+DWK DLY K+APH+A HAI ATNTSGL
Sbjct: 67  AARADYIAMANYGSDLEKLADCDLIIEAIAERLDWKLDLYAKIAPHVAEHAILATNTSGL 126

Query: 126 SITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTLGKGV 185
           SI  L+DG    L+ RFCG+HFFNPPRYM+LVELIPT  T+   LD LE FLTT LGKGV
Sbjct: 127 SIGKLADGVPEALRGRFCGIHFFNPPRYMYLVELIPTRYTEGAELDALETFLTTRLGKGV 186

Query: 186 VRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTADVVGL 245
           VRAKDTPNFIANR+G+FS+LA    AE+ GI FDVVDDLTG +LGR KSATFRTADVVGL
Sbjct: 187 VRAKDTPNFIANRIGVFSMLATIHHAERLGIRFDVVDDLTGPRLGRPKSATFRTADVVGL 246

Query: 246 DTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKVLDAK 305
           DT AHV+KTM D L DDP+   Y  PA ++ L++ GALGQKT  G Y+KEG+ I VLD K
Sbjct: 247 DTFAHVVKTMTDNLPDDPWHAFYTVPAWMQALIEKGALGQKTKGGIYRKEGRDIFVLDPK 306

Query: 306 TGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVYLEQI 364
           TG+YV +G+K D+ V  +LK ++ AE+ K LRES NPQAQFLWA  RDV+ YIA +L  I
Sbjct: 307 TGEYVQSGQKGDDEVKAILKIENPAEKFKALRESQNPQAQFLWACMRDVWQYIAYWLGDI 366

Query: 365 AGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWVFEGP 424
           AG+A D+D AIRWGFGW  GPFE WQ+AGWK +AE +  ++ AG+ +S+A LPAW     
Sbjct: 367 AGNARDVDFAIRWGFGWKQGPFEMWQAAGWKAIAEAISGEIAAGQTMSSAALPAW----- 421

Query: 425 VAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEENDAV 484
           V    GVH   GS+S A  S+ ARS LPVY+RQ +   + G A     + G T+ END V
Sbjct: 422 VNSVDGVHTPQGSYSAADNSYKARSTLPVYERQIYPPTVFGEAEP---QYGETIYENDGV 478

Query: 485 RIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLGAPGG 544
           R+W+  G DDV VV+FKSK +++G  V++GL  ++ +AEA Y GLV+W P +        
Sbjct: 479 RMWLRAG-DDVPVVTFKSKAHSVGAPVLEGLQASVRIAEARYPGLVIWHPEA-------- 529

Query: 545 PFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGGCELM 604
           PFS GA+L +  PAFM G    IE  V  FQ   M +KYA VPVV+AA G A GGGCE +
Sbjct: 530 PFSVGADLASMGPAFMTGDFDAIEKMVAEFQKTSMTIKYAQVPVVAAAQGYAFGGGCEFL 589

Query: 605 LHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSRFQSA 664
           +HSA  VAALE+YIGLVEVGVGL+PAGGG KE AL AAR A+     +IL  L   + + 
Sbjct: 590 MHSARVVAALESYIGLVEVGVGLLPAGGGCKEFALRAAREAKGG---DILAVLKDYYMAM 646

Query: 665 AMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPL-PTLVPVAG 723
           AMAKV+ SA E +++GYL+ SD +VFN +E+L+VAQ++VRALA AGY+AP+ P   PVAG
Sbjct: 647 AMAKVATSAEEGKEIGYLRESDIVVFNANEILHVAQSQVRALADAGYKAPIKPKGFPVAG 706

Query: 724 RSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALERKAFV 783
           R+G ATI+  L+NM +GGFIS +D+ I  +IAE VCGGDV+AG+LV+E+W+L LER+ F+
Sbjct: 707 RTGAATIRGQLINMLEGGFISKYDYHIGVQIAEVVCGGDVDAGTLVNEEWILTLERQRFM 766

Query: 784 DLLGTGKTQERIMGMLQTGKPVRN 807
            LL  GKTQERIM ML+  KP+RN
Sbjct: 767 GLLKKGKTQERIMYMLENNKPLRN 790


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: 1596
Number of extensions: 69
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: 790
Length adjustment: 41
Effective length of query: 766
Effective length of database: 749
Effective search space:   573734
Effective search space used:   573734
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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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:

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:

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:

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:

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