Aligments for a candidate for ech in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Aligments for a candidate for ech in Pseudomonas stutzeri RCH2

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 GFF4162 Psest_4235 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__psRCH2:GFF4162
          Length = 701

 Score =  206 bits (524), Expect = 3e-57
 Identities = 147/398 (36%), Positives = 222/398 (55%), Gaps = 30/398 (7%)

Query: 5   VIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKE-GVEQV 63
           VIG G MG GIA   A AG  V + +I+ E LQ+ ++R + + +   + GSL E  +EQ 
Sbjct: 300 VIGGGTMGVGIALSFANAGVPVKLLEINEEALQRGLQRARDTYAASVKRGSLTEDAMEQR 359

Query: 64  LARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISEI 123
           LA I   T+ A AL  +D V+EAV E++ +K+ +F   +A   P A+LA+NTSSL +  I
Sbjct: 360 LALIEGVTEYA-ALADADVVVEAVFEEMGVKQQVFEQLDAICKPGAILASNTSSLDLDAI 418

Query: 124 ASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVPG 183
           A+  K P+ VVG+HFF+P  +M L+E+VRG  TSDEV+ T   + K + K ++VV    G
Sbjct: 419 AAFTKRPEDVVGLHFFSPANVMRLLEVVRGAKTSDEVLATAMAIGKQLKKVSVVVGVCDG 478

Query: 184 FFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK- 242
           F  NR++ +      +L+E+G A+ Q+VD +A+   G  MG F + D +GLDIG ++ K 
Sbjct: 479 FVGNRMVFQYGREAEFLLEEG-ATPQQVD-AALRNFGMAMGPFAMRDLSGLDIGQAIRKR 536

Query: 243 -AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY------PSPGKFVRPTLPSTSKKL 295
              T      FP  S +KL + G LG K+G+GYY+Y      P     + P L + S + 
Sbjct: 537 QRATLPAHLDFPTVS-DKLCAAGMLGQKTGAGYYRYEPGNRTPQENPDLAPMLEAASLEK 595

Query: 296 G--------RYLIS----PAVNEVSYLLREGIVGK-DDAEKGCVLGLGLPK---GILSYA 339
           G        +Y++       VNE + +L EGI  +  D +   + G G P    G + YA
Sbjct: 596 GIERKALDEQYIVERCIFALVNEGAKILEEGIAQRSSDIDVIYLNGYGFPAFRGGPMFYA 655

Query: 340 DEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           D +G+D V+  ++E+    G D + P PLL  +  EG+
Sbjct: 656 DSVGLDRVLARVKELHARCG-DWWKPAPLLEKLAAEGR 692



 Score =  124 bits (311), Expect = 1e-32
 Identities = 85/228 (37%), Positives = 126/228 (55%), Gaps = 20/228 (8%)

Query: 398 TIVVRVEPP--LAWIVLNRPTRYNAINGDMIRE-INQALDSLEEREDVRVIAITGQGRVF 454
           T VVR+E    +A I +N P   NA+ G  +RE + +A  S E    VR +A+  +G  F
Sbjct: 2   TDVVRLEVQGEIALITVNNPP-VNAL-GQAVREGLQKAFQSAEADPQVRAVALVCEGNTF 59

Query: 455 SAGADVTEFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFR 514
            AGAD+ EFG      ++       EV   I+   K  +AVI+G ALGGG+E+AL   +R
Sbjct: 60  IAGADIKEFGKPPQAPSL------PEVIEIIEACNKSSVAVIHGTALGGGLEVALGCHYR 113

Query: 515 VASKTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFL 573
           +A K A++G PE+ LGL+PG GGTQRL RL+G  K LE++++G+ + A EA    IV+ L
Sbjct: 114 IARKDAKVGLPEVKLGLLPGAGGTQRLPRLAGVEKALEMIVSGQPISAAEAVEHNIVDEL 173

Query: 574 AEPEELESEVRKLANAIAEKSPLAVASAKLAYKLGEETHIWTGTSLEA 621
            E + +E+ +  +   + E         +   + GE+T    G   EA
Sbjct: 174 FEGDLVEAGLAYVRRMVEE--------GRTPRRTGEQTQGLEGADNEA 213



 Score = 26.9 bits (58), Expect = 0.003
 Identities = 21/95 (22%), Positives = 38/95 (40%), Gaps = 3/95 (3%)

Query: 295 LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEM 354
           +G  ++     E  +LL EG   +       +   G+  G  +  D  G+D+     +  
Sbjct: 480 VGNRMVFQYGREAEFLLEEGATPQQ--VDAALRNFGMAMGPFAMRDLSGLDIGQAIRKRQ 537

Query: 355 RQTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHTY 389
           R T    H     +   +   G LG+K+G G++ Y
Sbjct: 538 RATLPA-HLDFPTVSDKLCAAGMLGQKTGAGYYRY 571


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: 922
Number of extensions: 49
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: 701
Length adjustment: 39
Effective length of query: 612
Effective length of database: 662
Effective search space:   405144
Effective search space used:   405144
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:

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