Alignments for a candidate for ech in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Dinoroseobacter shibae DFL-12

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 3607421 Dshi_0835 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Dino:3607421
          Length = 737

 Score =  177 bits (448), Expect = 2e-48
 Identities = 127/400 (31%), Positives = 203/400 (50%), Gaps = 32/400 (8%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV- 60
           KV ++G+G+MG GIA ++A AG EV + D +    Q++ +R K   + + + G  ++ V 
Sbjct: 332 KVGILGAGMMGAGIAYVSANAGIEVVLIDAA----QESADRGKAHAAGILDKGIARKKVT 387

Query: 61  ----EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTS 116
               ++VLARI   TD A AL+G D V+EAV ED  +K  +   AEA     A+ ATNTS
Sbjct: 388 PEKKDEVLARITATTDYA-ALEGCDLVVEAVFEDPGVKAEVTAKAEAVIPGDAIFATNTS 446

Query: 117 SLPISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETI 176
           +LPISE+A     P++ +G+HFF+P   M LVEI++G+ T D  V    +  + + K  I
Sbjct: 447 TLPISELAKASARPEQFIGIHFFSPVDKMLLVEIIKGRQTGDVAVAKALDFVRQIRKTPI 506

Query: 177 VVKDVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDI 236
           VV D   F+ NR ++  +  G  +V +G+     +  +A + +G P+G   L D T +D+
Sbjct: 507 VVNDARFFYANRCIIPYINEGIRMVAEGVT--PALVENAAKLVGMPLGPLQLVDETSIDL 564

Query: 237 GYSVWKAVTARGFKAFPCSSTEK----LVSQGKLGVKSGSGYYQYPSPGKF--------- 283
           G  + KA  A    A+P  + ++    +  +G+LG KS +G+Y Y   GK          
Sbjct: 565 GVKIAKATKAAMGDAYPDGAVDEVLFWMADEGRLGRKSNAGFYTYDEAGKRGLLWEGLAD 624

Query: 284 ---VRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GILS 337
                   P  +    R L++  +  V  L    ++   + + G +LG G      G LS
Sbjct: 625 RYPAAKEQPELTAVQHRLLMAQVLEAVRALEDGVLMDIREGDVGAILGWGFAPWSGGPLS 684

Query: 338 YADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           + D IG    V   + +  T G    +P  LL  M ++G+
Sbjct: 685 WLDMIGAARAVEICDALTDTHGARFTTP-ALLREMAEKGE 723



 Score = 65.1 bits (157), Expect = 1e-14
 Identities = 50/180 (27%), Positives = 83/180 (46%), Gaps = 19/180 (10%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLT------PVKAM 472
           N +N     +++  +D     + V+ I IT     F+ G D+     +       P + +
Sbjct: 29  NVMNQQGFEDLDALVDKALADDTVKGIIITSGKDSFAGGMDLNVIAKMRDDAGDDPARGL 88

Query: 473 IAS-RKFHEVFMKIQFLT---------KPVIAVINGLALGGGMELALSAD--FRVASKTA 520
                  H +  KI+            KPV A + G ALG G+E+ L+    F   +  A
Sbjct: 89  FEGVMAMHGILRKIERAGMDPKTNKGGKPVAAALPGTALGIGLEIPLACHRIFAADNPKA 148

Query: 521 EMGQPEINLGLIPGGGGTQRLSR-LSGRKGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL 579
           ++G PEI +G+ PG GGT R+SR L   +   ++L G+  + ++A   GIV+ +   EEL
Sbjct: 149 KIGLPEIMVGIFPGAGGTMRVSRKLGAMQAAPILLEGKLFEPKKAKMAGIVDEVVPAEEL 208



 Score = 46.2 bits (108), Expect = 5e-09
 Identities = 34/93 (36%), Positives = 47/93 (50%), Gaps = 6/93 (6%)

Query: 300 ISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTSG 359
           I P +NE   ++ EG+      E    L +G+P G L   DE  ID+ V   +  +   G
Sbjct: 520 IIPYINEGIRMVAEGVTPAL-VENAAKL-VGMPLGPLQLVDETSIDLGVKIAKATKAAMG 577

Query: 360 MDHY---SPDPLLLSMVKEGKLGRKSGQGFHTY 389
            D Y   + D +L  M  EG+LGRKS  GF+TY
Sbjct: 578 -DAYPDGAVDEVLFWMADEGRLGRKSNAGFYTY 609


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: 1001
Number of extensions: 47
Number of successful extensions: 8
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: 737
Length adjustment: 39
Effective length of query: 612
Effective length of database: 698
Effective search space:   427176
Effective search space used:   427176
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
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