GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Pseudomonas fluorescens FW300-N2E3

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 AO353_00510 AO353_00510 multifunctional fatty acid oxidation complex subunit alpha

Query= BRENDA::A4YDS4
         (651 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00510 AO353_00510
           multifunctional fatty acid oxidation complex subunit
           alpha
          Length = 715

 Score =  182 bits (461), Expect = 6e-50
 Identities = 130/402 (32%), Positives = 198/402 (49%), Gaps = 32/402 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAM-ERIKWSLSKLRESGSLKEGV 60
           +  V+G+G+MG GIA  +A  G  + M DI+   ++Q + E  K  + ++ +       +
Sbjct: 316 QAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKLLVGRVDKGRMTAAKM 375

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
            +VL  I P           D V+EAV E+  +K+ +    E       +LA+NTS++ I
Sbjct: 376 AEVLNGIRPTLSYGD-FGHVDLVVEAVVENPNVKQAVLAEVEDKVKEGTILASNTSTISI 434

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           S +A  LK P+  VGMHFFNP  +MPLVE++RG+ +S++ + TT   AK M K  IVV D
Sbjct: 435 SLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSEQAIATTVAYAKKMGKNPIVVND 494

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
            PGF VNRVL         LV  G+  ++ +D   +E+ G+PMG   L D  G+D G+  
Sbjct: 495 CPGFLVNRVLFPYFGGFAKLVSAGVDFVR-ID-KVMEKFGWPMGPAYLMDVVGIDTGHH- 551

Query: 241 WKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQY-------------PSPGKF 283
            + V A GF    K    S+ + L    +LG K+G G+Y Y             PS  + 
Sbjct: 552 GRDVMAEGFPDRMKDDRRSAVDVLYEAKRLGQKNGKGFYAYETDKRGKQKKVADPSVLEV 611

Query: 284 VRPTL----PSTSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GI 335
           ++P +      T + +  +++ P   E    L +GIV    +A+ G V G+G P    G 
Sbjct: 612 LKPIVFEQREVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGA 671

Query: 336 LSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           L Y D IG+   V   ++      +  Y P   L  M K G+
Sbjct: 672 LRYIDAIGVAEFVALADQYADLGAL--YHPTAKLREMAKNGQ 711



 Score =  115 bits (288), Expect = 7e-30
 Identities = 60/172 (34%), Positives = 102/172 (59%), Gaps = 4/172 (2%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGS---LTPVKAMIAS 475
           N  N   + E+  A+D+++    V+ + ++    VF  GAD+TEF     L   + +  +
Sbjct: 30  NKFNRLTLNELRSAVDAIKADASVKGVIVSSGKDVFIVGADITEFVDNFKLPDAELVAGN 89

Query: 476 RKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEINLGLIPGG 535
            + +++F   + L  P +A ING+ALGGG+E+ L+AD+RV S TA++G PE+ LG+ PG 
Sbjct: 90  LEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADYRVMSTTAKIGLPEVKLGIYPGF 149

Query: 536 GGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRKL 586
           GGT RL R+ G    +E +  G+  + E+A ++G V+ +  PE+L+    +L
Sbjct: 150 GGTVRLPRIIGADNAIEWIAAGKENRPEDALKVGAVDAVVAPEQLQEAALEL 201


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: 64
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: 2
Length of query: 651
Length of database: 715
Length adjustment: 39
Effective length of query: 612
Effective length of database: 676
Effective search space:   413712
Effective search space used:   413712
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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