Alignments for a candidate for ech in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Thauera aminoaromatica S2

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_004300927.1 C665_RS04215 NAD-binding 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_000310185.1:WP_004300927.1
          Length = 671

 Score =  191 bits (486), Expect = 7e-53
 Identities = 132/346 (38%), Positives = 187/346 (54%), Gaps = 26/346 (7%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62
           V V+G+GVMG  IA + A+ G  V + D S E +  A+ R    L + R  G  ++ V  
Sbjct: 315 VHVVGAGVMGGDIAAVCALRGMTVTLQDQSVERIAPAIARAA-KLFERRHKGDARQ-VRF 372

Query: 63  VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122
            L R+ P+     A + +D +IEA+ E+LE+KR++F   EA A P AVLATNTSSL + +
Sbjct: 373 TLDRLIPDPKGEGAAR-ADVIIEAIFENLEVKRSLFAELEARAKPDAVLATNTSSLRLED 431

Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182
           IA+ LK P R+VG+HFFNP  ++PLVE+V+G+ T  EV++      + ++K  + VK  P
Sbjct: 432 IATALKDPSRLVGIHFFNPVPMLPLVEVVQGEATDAEVLRRATGFVRRIDKLPLPVKSAP 491

Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242
           GF VN VL   M      VE+G+A   E+  +A+   G PMG   L D  GLDI  +  K
Sbjct: 492 GFLVNSVLGPYMLEALRCVEEGVA--PEMVDAALVAFGMPMGPVELVDTVGLDIAVAAGK 549

Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFV----------------RP 286
           A+   G  A P +   KLV +GKLG KSG GYY++   GK V                RP
Sbjct: 550 ALAGEG--AEPPARLLKLVGEGKLGRKSGEGYYRWVD-GKAVKAGDEDERKGGLWRKRRP 606

Query: 287 T-LPSTSKKLGRYLISPAVNEVSYLLREGIVGKDD-AEKGCVLGLG 330
              P     L   +++P +      +  G+VG  D A+ G + G G
Sbjct: 607 APPPPIPAGLAERVLAPLLAATRRCVELGVVGDADLADAGVIFGTG 652



 Score =  102 bits (255), Expect = 4e-26
 Identities = 70/212 (33%), Positives = 112/212 (52%), Gaps = 7/212 (3%)

Query: 402 RVEPPLAWIVLNRP-TRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADV 460
           R E  LAW+ L++     N ++ D++ E    LD L+      ++  + +   F AGAD+
Sbjct: 16  REETGLAWLDLDKAEASANVLSADVLAEFAGVLDVLDAVPPKALVIASAKPAGFIAGADI 75

Query: 461 TEFGSLTPVKA--MIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVA-- 516
            EF  L  V A  M+  R +  +F ++  ++ P +A+I G  +GGG+ELAL+   R+   
Sbjct: 76  EEFSRLDSVLAARMLVERGWL-LFNRLAAVSYPTLALIRGHCMGGGLELALACRHRIVVD 134

Query: 517 SKTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAE 575
               ++  PE+ LG++PG GG  RL  L G    L+L+LTG+ V A++A RLG+ +    
Sbjct: 135 EPGTKLALPEVMLGIVPGWGGMLRLPALIGPAAALDLMLTGKSVDAKKAKRLGLADDCVP 194

Query: 576 PEELESEVRKLANAIAEKSPLAVASAKLAYKL 607
           P  +ES  R LA +   K PL      L + +
Sbjct: 195 PRVMESAARILALSGVAKKPLPFKERALRWAM 226



 Score = 45.8 bits (107), Expect = 6e-09
 Identities = 26/96 (27%), Positives = 47/96 (48%), Gaps = 6/96 (6%)

Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTS 358
           ++ P + E    + EG+    +     ++  G+P G +   D +G+D+ V   + +    
Sbjct: 498 VLGPYMLEALRCVEEGVA--PEMVDAALVAFGMPMGPVELVDTVGLDIAVAAGKALAGEG 555

Query: 359 GMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEA 394
                 P   LL +V EGKLGRKSG+G++ +   +A
Sbjct: 556 A----EPPARLLKLVGEGKLGRKSGEGYYRWVDGKA 587


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: 925
Number of extensions: 45
Number of successful extensions: 9
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: 671
Length adjustment: 38
Effective length of query: 613
Effective length of database: 633
Effective search space:   388029
Effective search space used:   388029
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 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:

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
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