Alignments for a candidate for ech in Klebsiella michiganensis M5al

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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Protein sequences (fasta format)
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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, or view the source code.

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