Aligments for a candidate for pimF in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__Marino:GFF1550 HP15_1512 multifunctional fatty
           acid oxidation complex subunit alpha
          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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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 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

GapMind for catabolism of small carbon sources