Alignments for a candidate for rhaD in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaD in Pedobacter sp. GW460-11-11-14-LB5

Align Lactaldehyde dehydrogenase (EC 1.2.1.22); Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate CA265_RS02630 CA265_RS02630 short-chain dehydrogenase

Query= reanno::Cola:Echvi_1572
         (702 letters)



>FitnessBrowser__Pedo557:CA265_RS02630
          Length = 706

 Score = 1006 bits (2601), Expect = 0.0
 Identities = 495/706 (70%), Positives = 583/706 (82%), Gaps = 4/706 (0%)

Query: 1   MSTAERTFKHVNYLWDEQKAQELEGDEVALLIYRSNILGADLRITNYGGGNTSCKTTEVD 60
           MS   +++KHV+YLWDE++A +L GDEVALLIYRSN+LGADLR+TNYGGGNTSCK  E D
Sbjct: 1   MSIDTKSYKHVSYLWDEEEAAKLAGDEVALLIYRSNLLGADLRLTNYGGGNTSCKVLEKD 60

Query: 61  PLTKEETEVMWVKGSGGDIGTLKRSGLAGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIY 120
           PLT  ETEVMWVKGSGGD+GTLK+SGLA LYV++L SLKN+YRG+E EDEMV LFNHCI+
Sbjct: 61  PLTGLETEVMWVKGSGGDLGTLKKSGLAALYVDRLRSLKNIYRGVEHEDEMVELFNHCIF 120

Query: 121 DLDSKAPSIDTPLHAFLPFKHIDHLHPDAAIAIAASKDGEKITEELFEGQIAWVPWQRPG 180
           DL SKAPSIDTPLH FLPF HIDHLHPDAAIAIAA+KDG+KITEELF G I WV W++PG
Sbjct: 121 DLSSKAPSIDTPLHGFLPFAHIDHLHPDAAIAIAAAKDGKKITEELFGGTIGWVEWKKPG 180

Query: 181 FDLALQLEKALNENPGIRGIMLGGHGLFTWGDTAYECYINSLEVIDKASEYLEQNYGKDR 240
           F+L LQL++ L+ENPGIRGIMLG HGLFTWGDTAYE Y+N+LEVI+  S+YL QNYGK  
Sbjct: 181 FELGLQLKQCLDENPGIRGIMLGSHGLFTWGDTAYESYLNTLEVIEICSDYLNQNYGKKG 240

Query: 241 PVFGGQKIESLAPEQRQEQASIIAPVLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLA 300
           PVFGGQKIES A +QR++QA+ +APVLRGL S    M+GHFTDD RVL+F NS+DL++LA
Sbjct: 241 PVFGGQKIESAAADQRKKQAAALAPVLRGLCSSKQHMIGHFTDDARVLEFINSNDLDRLA 300

Query: 301 PLGTSCPDHFLRTKIRPLVLDFPADVDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDN 360
           P+GTSCPDHFLRTKI PLVL   +D DLS    +KE L+  FE YRA Y  YYE  K  N
Sbjct: 301 PMGTSCPDHFLRTKISPLVLTLTSDADLSDVKALKETLEPAFEAYRAMYTAYYEACKHPN 360

Query: 361 SPAMRDPNPVVIIWPGVGMFSYAKNKQTARVASEFYINAINVMRGAEAVSEYVALPLQEA 420
           SPA+RD NPVVI++PG+GMF+++K+KQTARVA+EFYINAINVM+GAEAVS Y +LP QEA
Sbjct: 361 SPAIRDTNPVVILYPGIGMFTFSKDKQTARVAAEFYINAINVMKGAEAVSAYTSLPHQEA 420

Query: 421 FDIEYWLLEEAKLQRMPKEQPLSRKVALVTGGAGGIGKAIADKLASEGACVFITDINQER 480
           F+IEYWLLEEAKLQRMPK +PL+ K+AL+TG AGGIGKAIA K  +EG  V + D+N ER
Sbjct: 421 FNIEYWLLEEAKLQRMPKPKPLTGKIALITGSAGGIGKAIAKKFVAEGGVVILNDMNAER 480

Query: 481 LDGA----VATYSKDVGGGAVMDVTKGDDIIKAYKAAALKFGGVDIIVNCAGLAISKPIE 536
           L+ A       + KD    AV++VT  +DI +A+ +AAL FGGVDIIVN AGL+ISK I 
Sbjct: 481 LEEAAKEFAGLFGKDSYSTAVLNVTSEEDIKQAFDSAALAFGGVDIIVNNAGLSISKTIA 540

Query: 537 QTSEQDWDLLQDILVKGQFAVSKAGVETLRAQNLGGDIINIASKNALVSGPNNVGYGTAK 596
             +E+DWDLL D+LVKGQF +++A   T++ Q++GGDIINI SKNALVSGPNN GYG+AK
Sbjct: 541 DHTEKDWDLLYDVLVKGQFFITQAATNTMQKQDIGGDIINIVSKNALVSGPNNAGYGSAK 600

Query: 597 AAQVHMSRLLAAELGKDKIRVNVVNPDAVIEGSKIWEGEWAKGRAKAYGITVEELPAFYA 656
           AAQ+H+SRL AAELG D IRVNVVNPDAVI  S IW G WA+GRAKAYGITV ELPA+YA
Sbjct: 601 AAQLHLSRLNAAELGADNIRVNVVNPDAVISDSNIWAGGWAEGRAKAYGITVAELPAYYA 660

Query: 657 KRTILNEIIGVDDIANGVFAFVGGHLSKCTGNILNVDGGVAAAFVR 702
           KRT+LN+II  DDIAN  FAFVGG L K TGN+LNVDGGVA AFVR
Sbjct: 661 KRTLLNQIILPDDIANACFAFVGGLLHKSTGNVLNVDGGVAMAFVR 706


Lambda     K      H
   0.317    0.136    0.401 

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: 1409
Number of extensions: 58
Number of successful extensions: 2
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: 702
Length of database: 706
Length adjustment: 39
Effective length of query: 663
Effective length of database: 667
Effective search space:   442221
Effective search space used:   442221
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 (21.6 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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