GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Marinobacter adhaerens HP15

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate GFF1550 HP15_1512 multifunctional fatty acid oxidation complex subunit alpha

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__Marino:GFF1550
          Length = 715

 Score =  335 bits (858), Expect = 6e-96
 Identities = 226/677 (33%), Positives = 349/677 (51%), Gaps = 35/677 (5%)

Query: 39  NAAVADPAVQAIVLVCAGRTFIAGADITEF-----GKPPQPPA----LNDVIAALENSPK 89
           +A  A   ++ +V+  +  +FI GADITEF     G      A     N+V  A+E+ P 
Sbjct: 45  DALKAQKNLKGLVVTSSKDSFIVGADITEFTELFAGSEEDLVANNLKANEVFNAVEDLPF 104

Query: 90  PTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGLLPGAGGTQRLPRAVGPELA 149
           PT+ AI+G ALGGG E+ L   +RV  K+AK+GLPEVKLG+ PG GGT RL R VG + A
Sbjct: 105 PTVTAINGMALGGGFEMCLATDYRVMDKKAKVGLPEVKLGIFPGFGGTVRLSRLVGVDNA 164

Query: 150 VQMIVGGSPIGAAEALKHGLVEEVVEN--LVAGAVAFAKKVLAEKRPLRRLRDDDS---K 204
           V+ I GG+   A  ALK G V+ V+++  LV  AVA   +    K      R++     K
Sbjct: 165 VEWISGGTENRADVALKVGAVDAVLDSDKLVDAAVAIINQCNEGKLDHEARREEKKGKIK 224

Query: 205 LAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAIDLPFEEGLKKEREGFMKLVVS 264
           L A ++  +   +      K  +   AP      +     +  ++ ++ E +GF K+  +
Sbjct: 225 LNAMESMMAFEISKAFVAGKAGKNYPAPVEAIKVMQKHAGMTRDKAIEVEAKGFAKMAKT 284

Query: 265 DQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAGTMGGGIAMSFANAGIPVTLI 324
           + +      F  ++E  K     +  +   V+  A++GAG MGGG+A   A  G P+ + 
Sbjct: 285 NVAACLVGLFLNDQELKKKAKAWE-KEANDVNLAAVLGAGIMGGGVAFQSALKGTPIIMK 343

Query: 325 ETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALITGLVGLENVKDADLIIEAVFE 384
           +  ++ +  GL   +K       +G + PD  A  +  IT  +   + K+ DL++EAV E
Sbjct: 344 DINQDGIALGLKEAKKLLSKRVEKGKMKPDQMADVLNSITPTLNYGDFKNVDLVVEAVVE 403

Query: 385 TMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKRPQDVLGMHFFSPANVMKLCE 444
              VK  V    +   +   +L SNTS +SID +A   KRP++  GMHFF+P ++M L E
Sbjct: 404 NPKVKDAVLRETEDAVREDTILTSNTSTISIDLLAKNLKRPENFCGMHFFNPVHMMPLVE 463

Query: 445 IVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRMLAARSKQSEKLLFEGALPQQ 504
           ++RG KT+  A+ T V+ AK + K P+VV  C GF+ NR+L         L+ +GA  Q 
Sbjct: 464 VIRGEKTSDRAIATTVAYAKAMGKTPIVVNDCPGFLVNRVLFPYFGGFIGLVRDGADFQH 523

Query: 505 VDAVVTKFGMPMGPFAMGDLAGLDIGWRSRK-------DRGIKSE---IADALCEAGRFG 554
           VD V+ KFG PMGP  + D+ G+D G  + +       DR +K E     D + +  R+G
Sbjct: 524 VDKVMEKFGWPMGPAYLLDVVGMDTGKHAGEVMADGFPDR-MKHEGTTAIDVMFDNNRYG 582

Query: 555 QKTGKGYYKYE---QGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEILERMVYPMINE 611
           QK  KG+YKYE   +G +  + D E   L+   +      + + ++E+I+ RM+ P+  E
Sbjct: 583 QKNDKGFYKYELDRKGKQKKVVDEETYKLLEPVVQ----GKNEFSEEDIIARMMIPLCLE 638

Query: 612 GARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERLSAYAKATNDPS 671
             R LE+ I   P+D D+  ++G G+P +RGG + Y D +G+    E    +A     P 
Sbjct: 639 TVRCLEDGIVEDPADADMGLIFGIGFPPFRGGALRYIDDMGVDKFVELADKFADL--GPL 696

Query: 672 LEPAPLLARLAAEGKTF 688
             P   L  +A  GK F
Sbjct: 697 YHPTEKLREMAKTGKKF 713


Lambda     K      H
   0.317    0.134    0.383 

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: 1034
Number of extensions: 60
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 699
Length of database: 715
Length adjustment: 39
Effective length of query: 660
Effective length of database: 676
Effective search space:   446160
Effective search space used:   446160
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 (21.7 bits)
S2: 55 (25.8 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