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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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