GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimF in Shewanella loihica PV-4

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)

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



>lcl|FitnessBrowser__PV4:5210423 Shew_2864 3-hydroxyacyl-CoA
           dehydrogenase, NAD-binding (RefSeq)
          Length = 708

 Score =  629 bits (1623), Expect = 0.0
 Identities = 346/708 (48%), Positives = 468/708 (66%), Gaps = 27/708 (3%)

Query: 5   VTRATQDQV----AIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60
           +T AT  Q+    A++ ++ PPVN+L  A+R  +L ++  A AD +V AIVL  +G+ F 
Sbjct: 1   MTNATLYQIHGRTAVIILNQPPVNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFC 60

Query: 61  AGADITEFGKPPQ--PPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKE 118
            GADI+EF        P L  V  ALE SPK  +AA++G ALGGG E+ L C +R+A+  
Sbjct: 61  GGADISEFSSDDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPA 120

Query: 119 AKLGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE--- 175
           AKLGLPEV LG+LPGAGGTQRLPR  G +LA++MI  G P+GAA  L  G+++ + +   
Sbjct: 121 AKLGLPEVNLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNLYQDGG 180

Query: 176 NLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFAC 235
           N +  AV FA++++A+ +P R   +    +  +     IF    AA+ +++RG  AP  C
Sbjct: 181 NFIQAAVDFAQELVAQHKPKRSCFE--MSVDTSNISSEIFNEFRAAIARRSRGYYAPERC 238

Query: 236 ADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGV-PDGTKPRP 294
             A+ AA +LP  EGLK+E + FM+ + + Q++AQ++ FFAER  AK+ G+ P  T  R 
Sbjct: 239 IQAVEAACELPLAEGLKREHQLFMECLDTPQARAQQHLFFAERGVAKIPGINPKTTATRE 298

Query: 295 VSRVAIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPD 354
           + +VA+IG+GTMGGGIAM+F N GIP  +++   E L+RGLG+++KN+E T  +G L   
Sbjct: 299 IRKVAVIGSGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQA 358

Query: 355 APAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLS 414
              +RMAL++G     ++ D DL+IEAVFE M +KK+VF  +DA  KPGA+LA+NTS L 
Sbjct: 359 QLDERMALLSGTTDYADIADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLD 418

Query: 415 IDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVG 474
           +DEIAA T RPQDVLG+HFFSPANVM+L EIVR  KTAPDALLT V +A++I KVPVV G
Sbjct: 419 VDEIAAETSRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSG 478

Query: 475 VCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSR 534
           VC GF+GNR   +  ++S  L+ EGA P Q+D V T+FGMPMG  +M DLAG+D+G  +R
Sbjct: 479 VCWGFIGNRATDSYLRESMSLILEGASPAQIDKVHTEFGMPMGLPSMVDLAGIDVGILTR 538

Query: 535 KDRGIKS--------EIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLA 586
           +DR   +         I   L    R+GQKTG+G Y YE   R    DPEV  L  +   
Sbjct: 539 EDRKAFTTDLDPSHFAILHKLYAKQRYGQKTGRGLYIYE--GRDKQEDPEVLELAAEAAK 596

Query: 587 KLGLKRR---DITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGG 643
           + G+ RR    I+D+EILER +YP+INEGARILEE IA R SDID+V  YG+G+PI+RGG
Sbjct: 597 EFGVTRRSPEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFPIFRGG 656

Query: 644 PMHYADSVGLKHIAERLSAYAKATNDPSL--EPAPLLARLAAEGKTFA 689
           PM YAD +GL+ +   L+ Y    +   L  +PAPLL RL  EGKTFA
Sbjct: 657 PMQYADEIGLERVLTALNKYRDTLDKGELWFKPAPLLERLVKEGKTFA 704


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: 1089
Number of extensions: 57
Number of successful extensions: 6
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: 708
Length adjustment: 39
Effective length of query: 660
Effective length of database: 669
Effective search space:   441540
Effective search space used:   441540
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 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