GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Shewanella sp. ANA-3

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 7022769 Shewana3_0024 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

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



>FitnessBrowser__ANA3:7022769
          Length = 716

 Score =  348 bits (893), Expect = e-100
 Identities = 239/680 (35%), Positives = 344/680 (50%), Gaps = 27/680 (3%)

Query: 10  QDQVAIVTVDSP-PVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEF 68
           +D +A +  ++P  VN         +   +++      +QA+VL     TFI GADITEF
Sbjct: 14  EDNIAKLCFNAPGSVNKFDRETLASLDAALDSIKQQSNIQALVLTSGKDTFIVGADITEF 73

Query: 69  -GKPPQPPAL--------NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEA 119
            G   Q  A+        N V   LE+ P PT +AI G ALGGG E  L   FR+A   A
Sbjct: 74  LGLFAQDDAVLLSWIEQANAVFNKLEDLPFPTASAIKGFALGGGCETILATDFRIADTTA 133

Query: 120 KLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVV--ENL 177
           K+GLPE KLG++PG GGT RLPR +G + A++ I  G      +ALK G V+ VV  E L
Sbjct: 134 KIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGKDQRPEDALKVGAVDAVVAPEAL 193

Query: 178 VAGAVAFAKKVLAEK---RPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFA 234
            A A+   K  +AEK   +  R+ +     L   +A  S  T          +   AP A
Sbjct: 194 EAAAIQMLKDAVAEKLDWQARRQRKMSPLTLPKLEAMMSFTTAKGMVFAVAGKHYPAPMA 253

Query: 235 CADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRP 294
               +  A      + L+ E + F+KL  +D +KA     F   +  K      G   + 
Sbjct: 254 AVSVVEQAATKGRSDALQIEHQAFIKLAKTDVAKAL-IGIFLNDQLVKGKAKKAGKLAKD 312

Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354
           V   A++GAG MGGGIA   A+ G P+ + +  +  L  GLG   K   A  ARG   P+
Sbjct: 313 VKSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDLGLGEAAKLLSAQVARGRSTPE 372

Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414
             AK +  IT  +    VK AD+++EAV E   VK +V   V+ +    A++ASNTS +S
Sbjct: 373 KMAKVLNNITPALDYAPVKHADVVVEAVVEHPKVKAQVLAEVEQYVSEDAIIASNTSTIS 432

Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474
           I+ +A + K+P+   GMHFF+P + M L E++RG  ++ + + + V+ A K+ K P+VV 
Sbjct: 433 INLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSEETIASVVAYASKMGKTPIVVN 492

Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTK-FGMPMGPFAMGDLAGLDIGWRS 533
            C GF  NR+L         LL EG     +D V+ K FG PMGP  + D+ GLD G  +
Sbjct: 493 DCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQFGWPMGPAYLLDVVGLDTGHHA 552

Query: 534 R-------KDRGIKS--EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDT 584
           +        DR  KS  +  D + E  R GQK GKG+Y Y   SR   P  +V+    + 
Sbjct: 553 QAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYAYSVDSRG-KPKKDVDPTSYEL 611

Query: 585 LAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGP 644
           L     +++    +EI+ R + PMI E  R LEE I A P++ D+  +YG G+P +RGG 
Sbjct: 612 LKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVASPAEADMGLVYGLGFPPFRGGV 671

Query: 645 MHYADSVGLKHIAERLSAYA 664
             Y D++G+ +       YA
Sbjct: 672 FRYLDTMGVANFVALADKYA 691


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: 1068
Number of extensions: 57
Number of successful extensions: 7
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: 716
Length adjustment: 39
Effective length of query: 660
Effective length of database: 677
Effective search space:   446820
Effective search space used:   446820
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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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