Alignments for a candidate for pimF in Marinobacter adhaerens HP15

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 GFF4001 HP15_3941 fatty oxidation complex alpha subunit

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



>FitnessBrowser__Marino:GFF4001
          Length = 702

 Score =  726 bits (1873), Expect = 0.0
 Identities = 380/698 (54%), Positives = 486/698 (69%), Gaps = 8/698 (1%)

Query: 1   MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60
           MSEVV+   +  + ++TV+ PPVNAL  AVR G+L  +     D   +A++LVC GRTFI
Sbjct: 6   MSEVVSYNREGNIGVITVNYPPVNALGQAVRSGLLAALEQGQKDTEARALLLVCEGRTFI 65

Query: 61  AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120
           AGADI EFGKP Q P L  ++   ENS KP +AAIHGTALGGGLE AL CH+RVA+  AK
Sbjct: 66  AGADIREFGKPMQEPTLPTLVNTFENSDKPLVAAIHGTALGGGLETALSCHYRVAISSAK 125

Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE--NLV 178
           +GLPEVKLGLLPGAGGTQRLPR  G   A++MI  G  +GA +AL  G+++ V E  ++ 
Sbjct: 126 VGLPEVKLGLLPGAGGTQRLPRLTGARKALEMITTGEFVGAKDALALGILDAVEEGDDIR 185

Query: 179 AGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADA 238
           A  +A+A+KV+ E +P+RR+RD   K+ A K    +F      + K+ARGL +PF C DA
Sbjct: 186 AVGMAYAQKVVDEGKPVRRVRDITDKIEADKGS-DVFDQFRDELKKRARGLFSPFKCVDA 244

Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298
           + AA +LPF+EG+K+ERE FM+ + S Q     ++FF ERE +KV G+   T  R V  V
Sbjct: 245 VEAAFNLPFDEGMKRERELFMECMESPQRAGLIHSFFGEREVSKVKGLSKDTPVRDVKSV 304

Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAK 358
            IIGAGTMGGGIAM+F N GIPVT++E  +E L +GL I+++N+E +A +G L  +   +
Sbjct: 305 GIIGAGTMGGGIAMNFVNVGIPVTIVEVKQEALDKGLAIIRRNYENSAKKGKLTQEQVEQ 364

Query: 359 RMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEI 418
           RMALIT  +  ++ +D DL+IEAVFE MA+KKE+F  +D   KPGA+LASNTS L IDEI
Sbjct: 365 RMALITPSLTYDDFRDVDLVIEAVFENMAIKKEIFAKLDEVCKPGAILASNTSTLDIDEI 424

Query: 419 AATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDG 478
           A+ TKRP+DV+GMHFFSPANVMKL E VRG+KT+ +   T +++AKKI KV V+VG C G
Sbjct: 425 ASATKRPEDVVGMHFFSPANVMKLLENVRGSKTSDEVKATVMAVAKKIKKVGVMVGNCYG 484

Query: 479 FVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDR- 537
           FVGNRML  R  ++  L+ EGA PQQVD V+T  G PMG FAM DLAG+D+G+R R++R 
Sbjct: 485 FVGNRMLHKRGTEAMSLVDEGATPQQVDKVLTDLGFPMGQFAMSDLAGIDVGYRIREERR 544

Query: 538 ----GIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRR 593
                I +   D L E GR GQKT  G YKYE+GSR P+PDPEVE LI     + G+  R
Sbjct: 545 KAGEDIPASWMDKLAEQGRLGQKTQAGVYKYEEGSRKPIPDPEVEQLIEQFRKEQGITPR 604

Query: 594 DITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGL 653
           +IT++EILER VY MINEGA+ILEE IA RP DID+VW+YGYG+P YRGGPM +AD  GL
Sbjct: 605 EITNQEILERCVYVMINEGAKILEEGIADRPLDIDIVWIYGYGFPAYRGGPMFWADQEGL 664

Query: 654 KHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFASL 691
             I   +  Y         EPA LL +L AEG+ FA L
Sbjct: 665 DTILSAVKKYQDTVGGEQWEPAALLEKLVAEGRKFADL 702


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: 1172
Number of extensions: 65
Number of successful extensions: 4
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: 702
Length adjustment: 39
Effective length of query: 660
Effective length of database: 663
Effective search space:   437580
Effective search space used:   437580
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: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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