GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Klebsiella michiganensis M5al

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 BWI76_RS01365 BWI76_RS01365 multifunctional fatty acid oxidation complex subunit alpha

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Koxy:BWI76_RS01365
          Length = 729

 Score =  183 bits (465), Expect = 2e-50
 Identities = 128/367 (34%), Positives = 187/367 (50%), Gaps = 33/367 (8%)

Query: 5   VIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ-- 62
           V+G+G+MG GIA  +A  G  V M DI+ + L   M      L+K  E G + +G++   
Sbjct: 318 VLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERGKI-DGLKMAG 376

Query: 63  VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122
           V++ I P  D A   +  D V+EAV E+ ++K+ +    E    P  VLA+NTS++PISE
Sbjct: 377 VISTIQPTLDYA-GFERVDVVVEAVVENPKVKKAVLAETEEKVRPDTVLASNTSTIPISE 435

Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182
           +ASVL+ P+   GMHFFNP   MPLVE++RG  TSD+ +      A  M K  IVV D P
Sbjct: 436 LASVLQRPENFCGMHFFNPVHRMPLVEVIRGDKTSDKTIAKVVAWASKMGKTPIVVNDCP 495

Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242
           GFFVNRVL         L+  G A  ++VD    ++ G+PMG   L D  G+D  +   +
Sbjct: 496 GFFVNRVLFPYFAGFSQLLRDG-ADFRKVDKVMEKQFGWPMGPAYLLDVVGIDTAHHA-Q 553

Query: 243 AVTARGF-----KAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGK--------------- 282
           AV A GF     K +   + + L    + G K+G G+++Y    K               
Sbjct: 554 AVMAAGFPQRMQKEYR-DAIDALFDAKRFGQKNGLGFWRYKEDSKGKPKKEEDTVVDSLL 612

Query: 283 --FVRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---GIL 336
               +P    + +++   ++ P VNEV   L EGI+    +A+   V GLG P    G  
Sbjct: 613 AEVSQPKRDFSDEEIIARMMIPMVNEVVRCLEEGIIASPAEADMALVYGLGFPPFHGGAF 672

Query: 337 SYADEIG 343
            + D +G
Sbjct: 673 RWLDTLG 679



 Score =  114 bits (284), Expect = 2e-29
 Identities = 62/180 (34%), Positives = 107/180 (59%), Gaps = 4/180 (2%)

Query: 404 EPPLAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEF 463
           E  +A +V + P   N ++   +  + +ALD LE+++D++ + +  +   F  GAD+TEF
Sbjct: 14  EDGIAELVFDAPGSVNKLDTATVASLGEALDVLEKQKDLKGLLLRSEKAAFIVGADITEF 73

Query: 464 GSLTPVKAMIASRKFH---EVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTA 520
            SL  V     S+  H    VF +++ L  P I+ +NG ALGGG E  L+ D+R+A+   
Sbjct: 74  LSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCECVLATDYRLATPDL 133

Query: 521 EMGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL 579
            +G PE  LG++PG GG+ R+ R+ G    LE++  G+ + AE+A ++G+V+ + + E+L
Sbjct: 134 RIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDLGAEQALKIGLVDGVVKHEKL 193


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: 1035
Number of extensions: 55
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 651
Length of database: 729
Length adjustment: 39
Effective length of query: 612
Effective length of database: 690
Effective search space:   422280
Effective search space used:   422280
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 Sep 17 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