GapMind for catabolism of small carbon sources

 

Alignments 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:

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