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

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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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 paper from 2022 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