GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Methylocapsa aurea KYG

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate WP_036259721.1 DL86_RS06940 fatty acid oxidation complex subunit alpha FadB

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_000746085.1:WP_036259721.1
          Length = 720

 Score =  190 bits (483), Expect = 2e-52
 Identities = 130/374 (34%), Positives = 196/374 (52%), Gaps = 31/374 (8%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60
           K  V+G+GVMG GIA  +A  G  + M DI+ + L   M   +  L++  E G L +   
Sbjct: 319 KAAVVGAGVMGGGIAYQSAARGVPIIMKDIAEQALDLGMSEARKLLARQVEQGRLDQAKA 378

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           + +L  I P     +   G D VIEAV E++ +K+ +    E     +A+LA+NTSSL I
Sbjct: 379 DAILGAIAPGLTY-EGFDGVDVVIEAVVENIAVKKAVLSELERVTGEAAILASNTSSLRI 437

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
            ++   L+ P + +GMHFFNP   M LVE+VRG  TS+E + T    A +M K  IV++D
Sbjct: 438 GDLTEGLRRPDKFIGMHFFNPVPRMALVEVVRGPKTSEETIATIVGYADAMGKTPIVMQD 497

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
            PGF VNR L   + A   LV  G A    VD   +E  G+PMG   L D  G+DI + V
Sbjct: 498 CPGFVVNRALTPYLIAFLRLVHDG-ADFAHVD-KVMETFGWPMGPAYLIDVIGMDISHHV 555

Query: 241 WKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQY-------------PSPGKF 283
            + V+A GF    +    S+ + L+ + +LG K+G G+Y+Y             P   + 
Sbjct: 556 VEIVSA-GFPERMQTSFASAIDILLREKRLGQKNGHGFYKYAKDAKGRPRKELDPETDRL 614

Query: 284 VRPTLPSTSKKLG-----RYLISPAVNEVSYLLREGIVG-KDDAEKGCVLGLGLPK---G 334
           +    P+    +G       ++ P + E +  + +G+VG + +A+   +LGLGLP+   G
Sbjct: 615 LAEARPNGKIAIGEDEIVERMMLPLIFEAARCVEDGVVGSRGEADMSLILGLGLPRYLGG 674

Query: 335 ILSYADEIGIDVVV 348
            L YAD +G+  VV
Sbjct: 675 ALKYADHLGVANVV 688



 Score =  103 bits (258), Expect = 2e-26
 Identities = 63/169 (37%), Positives = 92/169 (54%), Gaps = 8/169 (4%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL-----TPVKAMI 473
           N ++     E+ +AL+ +     ++ + I      F  GAD+ EF ++       + A +
Sbjct: 34  NKLDALTFSELRRALEIIAATPAIKGVLIASAKDAFIVGADIFEFTAIFKRPPEDIVAFV 93

Query: 474 ASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEINLGLIP 533
           A     E+   +  L  P +A INGLALGGG+ELAL+ADFRV S  A +G PE++LGL P
Sbjct: 94  AQNS--EIITALADLPVPTVAAINGLALGGGLELALAADFRVMSSAARIGFPEVHLGLFP 151

Query: 534 GGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELES 581
           G GGT RL RL G     E + +G + K E A   G V+ +  PE+L +
Sbjct: 152 GYGGTVRLPRLIGLVASAEWIASGAQQKPEAALEEGAVDAVVAPEDLRA 200



 Score = 30.0 bits (66), Expect = 4e-04
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 13/70 (18%)

Query: 330 GLPKGILSYADEIGIDVVVNTLE-------EMRQTSGMDHYSPDPLLLSMVKEGKLGRKS 382
           G P G     D IG+D+  + +E       E  QTS     S   +LL   +E +LG+K+
Sbjct: 535 GWPMGPAYLIDVIGMDISHHVVEIVSAGFPERMQTS---FASAIDILL---REKRLGQKN 588

Query: 383 GQGFHTYAHE 392
           G GF+ YA +
Sbjct: 589 GHGFYKYAKD 598


Lambda     K      H
   0.316    0.134    0.377 

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: 977
Number of extensions: 51
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 720
Length adjustment: 39
Effective length of query: 612
Effective length of database: 681
Effective search space:   416772
Effective search space used:   416772
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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