GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Magnetospirillum magneticum AMB-1

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_011385366.1 AMB_RS15050 multifunctional fatty acid oxidation complex subunit alpha

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



>NCBI__GCF_000009985.1:WP_011385366.1
          Length = 703

 Score =  598 bits (1541), Expect = e-175
 Identities = 323/697 (46%), Positives = 450/697 (64%), Gaps = 10/697 (1%)

Query: 1   MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60
           MS+VVT +  D++A VT+DSPPVNA    VR G+ +      A     A++++CAGRTF+
Sbjct: 1   MSDVVTLSVSDRIATVTIDSPPVNAADHPVRAGLQKVFTDLAARSDYDAVLVLCAGRTFM 60

Query: 61  AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120
           AGADI EF    + P   D+   +EN  KP +AA+HGTALG G E+A+ CH+R+A K A+
Sbjct: 61  AGADIGEFDTGIKAPHHQDLFNLVENCAKPVVAALHGTALGAGTELAMACHYRIADKGAR 120

Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVA 179
           +GLPE+ LG++PGAGGTQR PR +G + A+ +++ G P+ A +A + GLV+E+   +L A
Sbjct: 121 IGLPELSLGIIPGAGGTQRAPRLIGLDAAMDLVLSGKPLPAPKAAELGLVDEIASGDLNA 180

Query: 180 GAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAI 239
            A+AFAKK++AE + +RR  D   K AA  A+      A  A T K R   +P    +A+
Sbjct: 181 AALAFAKKLVAEGKGVRRTCDMAPKDAAKDAEIIAARQAQVAKTMKNR--TSPLKALEAM 238

Query: 240 GAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVA 299
            A   L F EGL+ E +   +L  + +++A R+ FFA+RE  K+ G+    K RP+ +V 
Sbjct: 239 AATTTLSFAEGLRLEADISKQLEHAVEARAMRHLFFADREVRKIPGITKDIKARPIRKVG 298

Query: 300 IIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKR 359
           IIGAGTMGGGIAM FAN GIPVT+I+  +E L+RGLG+++KN+E + +RG L  +    R
Sbjct: 299 IIGAGTMGGGIAMCFANIGIPVTIIDVSDENLQRGLGVIRKNYERSVSRGSLTQEQLESR 358

Query: 360 MALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIA 419
           M L++       +KDADL IEAVFE M +KK++F  +DA    GA+L +NTS L IDEIA
Sbjct: 359 MGLLSASTDYAALKDADLAIEAVFEKMELKKDIFAKLDAVLPAGAILGTNTSTLDIDEIA 418

Query: 420 ATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGF 479
            TTKRP DV+G+HFFSPANVM L EIV+G +TA D LLTA+ +AK I K  VV  VC GF
Sbjct: 419 NTTKRPADVIGLHFFSPANVMPLLEIVQGKQTAMDVLLTALDMAKLIKKTGVVSKVCYGF 478

Query: 480 VGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR----- 534
           +GNRM+    +++E+++ EGA P ++D  +  +GM MG  A+ D+AG+++G  +R     
Sbjct: 479 IGNRMMDPYGREAERMVLEGATPAEIDGALEGWGMAMGILAVYDMAGVEVGDNTRIANPH 538

Query: 535 --KDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKR 592
              D       +  L      GQK G+GYY+Y+   R    DPEV  +++    +L +  
Sbjct: 539 MVPDDPSFYRCSTLLVANKWLGQKVGRGYYRYDSPDRKRASDPEVIEMMHAEGKRLNVPA 598

Query: 593 RDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVG 652
           R    +EILER +Y MINEGA++LEE IA R SDIDVV+  GYG+P YRGGPM YAD++G
Sbjct: 599 RKPGKDEILERCLYSMINEGAKLLEEGIALRASDIDVVYTAGYGFPRYRGGPMFYADTIG 658

Query: 653 LKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTFA 689
           LK I +++  + K  +     PAPLL +LA  G TFA
Sbjct: 659 LKVIYDKIVEFQKTLDPRYWTPAPLLEKLAKAGSTFA 695


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: 1140
Number of extensions: 52
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: 703
Length adjustment: 39
Effective length of query: 660
Effective length of database: 664
Effective search space:   438240
Effective search space used:   438240
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.

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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