Alignments for a candidate for ech in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Shewanella loihica PV-4

Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)

Query= SwissProt::Q08426
         (723 letters)



>FitnessBrowser__PV4:5210423
          Length = 708

 Score =  455 bits (1171), Expect = e-132
 Identities = 282/710 (39%), Positives = 397/710 (55%), Gaps = 27/710 (3%)

Query: 6   RLHNALALIRLRNPPVNAISTTLLRDIKEGLQKAVIDHTIKAIVICGAEGKFSAGADIRG 65
           ++H   A+I L  PPVN++   L   +   L++A  D ++ AIV+  +   F  GADI  
Sbjct: 8   QIHGRTAVIILNQPPVNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISE 67

Query: 66  FSAPRTFGL-TLGHVVDEIQRNEKPVVAAIQGMAFGGGLELALGCHYRIAHAEAQVGLPE 124
           FS+        L  V D ++ + K VVAA+ G+A GGG EL L C YRIA   A++GLPE
Sbjct: 68  FSSDDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPE 127

Query: 125 VTLGLLPGARGTQLLPRLTGVPAALDLITSGRRILADEALKLGILDKVVNSDP--VEEAI 182
           V LG+LPGA GTQ LPR+ GV  AL++ITSGR + A   L  G++D +       ++ A+
Sbjct: 128 VNLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNLYQDGGNFIQAAV 187

Query: 183 RFAQRVSDQPLESRRLCNKPIQSLPNMDSIFSEALLKMRRQHPGCLAQEACVRAVQAAVQ 242
            FAQ +  Q    R      + +      IF+E    + R+  G  A E C++AV+AA +
Sbjct: 188 DFAQELVAQHKPKRSCFEMSVDTSNISSEIFNEFRAAIARRSRGYYAPERCIQAVEAACE 247

Query: 243 YPYEVGIKKEEELFLYLLQSGQARALQYAFFAERKANKWSTPSGASWKTASARPVSSVGV 302
            P   G+K+E +LF+  L + QARA Q+ FFAER   K     G + KT + R +  V V
Sbjct: 248 LPLAEGLKREHQLFMECLDTPQARAQQHLFFAERGVAKIP---GINPKTTATREIRKVAV 304

Query: 303 VGLGTMGRGIVISFARARIPVIAVDSDKNQLATANKMITSVLEKEASKMQQSGHPWSGPK 362
           +G GTMG GI ++F    IP   +D +   L     +I    E    K + S        
Sbjct: 305 IGSGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQAQLDERM 364

Query: 363 PRL--TSSVKELGGVDLVIEAVFEEMSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIAS 420
             L  T+   ++  VDLVIEAVFE+M +KKQVF  L A CKP A L TNTS LDVDEIA+
Sbjct: 365 ALLSGTTDYADIADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLDVDEIAA 424

Query: 421 STDRPHLVIGTHFFSPAHVMKLLEVIPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGFV 480
            T RP  V+G HFFSPA+VM+LLE++ +  ++P  + T + L+++IKK+ VV G C+GF+
Sbjct: 425 ETSRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSGVCWGFI 484

Query: 481 GNRMLNPYYNQAYFLLEEGSKPEEVDQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGLT 540
           GNR  + Y  ++  L+ EG+ P ++D+V  EFG  MG   + DLAG+DVG  +R+ +   
Sbjct: 485 GNRATDSYLRESMSLILEGASPAQIDKVHTEFGMPMGLPSMVDLAGIDVGILTREDRKAF 544

Query: 541 GPTLLPGTPARKRGNRRYCPIPDVLCELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKFL 600
              L P           +  I   L    R+GQKTG+G Y Y+   GR  + DP + +  
Sbjct: 545 TTDLDPS----------HFAILHKLYAKQRYGQKTGRGLYIYE---GRDKQEDPEVLELA 591

Query: 601 SRYRKTHHI---EPRTISQDEILERCLYSLINEAFRILGEGIAASPEHIDVVYLHGYGWP 657
           +   K   +    P  IS  EILER +Y +INE  RIL EGIA     ID+V  +G+G+P
Sbjct: 592 AEAAKEFGVTRRSPEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFP 651

Query: 658 RHKGGPMFYASTVGLPTVLEKLQKYYRQNPDIPQL--EPSDYLKKLASQG 705
             +GGPM YA  +GL  VL  L K YR   D  +L  +P+  L++L  +G
Sbjct: 652 IFRGGPMQYADEIGLERVLTALNK-YRDTLDKGELWFKPAPLLERLVKEG 700


Lambda     K      H
   0.319    0.136    0.405 

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: 1124
Number of extensions: 50
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: 723
Length of database: 708
Length adjustment: 39
Effective length of query: 684
Effective length of database: 669
Effective search space:   457596
Effective search space used:   457596
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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:

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
the source code
instructions for running GapMind on your computer

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