Alignments for a candidate for aldA in Streptomyces kebangsaanensis SUK12

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Streptomyces kebangsaanensis SUK12

Align Lactaldehyde dehydrogenase (EC 1.2.1.22); Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate WP_073952102.1 RH94_RS33590 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

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



>NCBI__GCF_001906585.1:WP_073952102.1
          Length = 679

 Score =  667 bits (1722), Expect = 0.0
 Identities = 345/683 (50%), Positives = 454/683 (66%), Gaps = 16/683 (2%)

Query: 27  EVALLIYRSNILGADLRITNYGGGNTSCKTTEVDPLTKEETEVMWVKGSGGDIGTLKRSG 86
           E   L+ RS+ LGAD R TNY GGNTS K T+ DP+T  + E+MWVKGSGGD+GTL  +G
Sbjct: 6   EAEALLSRSHRLGADSRNTNYAGGNTSAKGTDTDPVTGGDVELMWVKGSGGDLGTLTEAG 65

Query: 87  LAGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIYDLDSKAPSIDTPLHAFLPFKHIDHLH 146
           LA L +++L +LK+VY G+E EDEMV  F++C++     APSIDT +H  +   H+DHLH
Sbjct: 66  LAVLRLDRLRALKDVYPGVEREDEMVAAFDYCLHGKGGAAPSIDTAMHGLVDAPHVDHLH 125

Query: 147 PDAAIAIAASKDGEKITEELFEGQIAWVPWQRPGFDLALQLEKALNENPGIRGIMLGGHG 206
           PD+ IA+A + DGEK+T E F  ++ WVPW+RPGF L L +      NP   G +LGGHG
Sbjct: 126 PDSGIALACAADGEKLTAECFGDRVVWVPWRRPGFQLGLDIAAVQEANPQAIGCVLGGHG 185

Query: 207 LFTWGDTAYECYINSLEVIDKASEYLEQNYGKDRPVFGG--QKIESLAPEQRQEQASIIA 264
           +  WG T+ EC  NSL +I  A  +L +  G+  P FG   +  E+L   +R+E+A+ +A
Sbjct: 186 ITAWGATSEECERNSLHIIRTAEAFLTER-GRPEP-FGAVIEGYEALPGGERRERAAALA 243

Query: 265 PVLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLAPLGTSCPDHFLRTKIRPLVLDFPA 324
           P +R LAS     VGHF D + VL F +  +  +LA LGTSCPDHFLRTK+RPLVLD P 
Sbjct: 244 PYVRALASRDKAQVGHFDDADVVLDFLSRAEHPRLAALGTSCPDHFLRTKVRPLVLDLPP 303

Query: 325 DVDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDNSPAMRDPNPVVIIWPGVGMFSYAK 384
              L    E  ++L +   EYR  Y  YYE H   +SPAMR  +P +++ PGVGMFS+ K
Sbjct: 304 TAPL---QETVDRLQELHAEYREEYAAYYERHALPDSPAMRGADPAIVLVPGVGMFSFGK 360

Query: 385 NKQTARVASEFYINAINVMRGAEAVSEYVALPLQEAFDIEYWLLEEAKLQRMPKEQPLSR 444
           +KQTARVA EFY+NAINVMRGAEAVS Y  +   E F IEYW LEEAKL+RMP+ +PL+ 
Sbjct: 361 DKQTARVAGEFYVNAINVMRGAEAVSTYAPIEESEKFRIEYWALEEAKLRRMPEPRPLAT 420

Query: 445 KVALVTGGAGGIGKAIADKLASEGACVFITDINQERLDGAVATYSKDVGG-----GAVMD 499
           +VALVTG   GIGKAIA +L +EGACV + D+N        A  ++++GG        +D
Sbjct: 421 RVALVTGAGSGIGKAIAHRLVAEGACVVVADLNARN----AAAVAEELGGPDKAVAVTVD 476

Query: 500 VTKGDDIIKAYKAAALKFGGVDIIVNCAGLAISKPIEQTSEQDWDLLQDILVKGQFAVSK 559
           VT  + I  A++AA L FGGVD++VN AG+++SKP+ +TS +DWDL   ++ +G F VS+
Sbjct: 477 VTDEEQIAGAFEAALLAFGGVDLVVNNAGISLSKPLLETSAEDWDLQHAVMARGSFLVSR 536

Query: 560 AGVETLRAQNLGGDIINIASKNALVSGPNNVGYGTAKAAQVHMSRLLAAELGKDKIRVNV 619
                + AQ LGGDI+ IASKNA+ +GP+N+ Y   KA Q H  RLLAAELG+  IRVN 
Sbjct: 537 EAARVMIAQRLGGDIVYIASKNAVFAGPDNIAYSATKADQAHQVRLLAAELGEHGIRVNG 596

Query: 620 VNPDAVIEGSKIWEGEWAKGRAKAYGITVEELPAFYAKRTILNEIIGVDDIANGVFAFVG 679
           VNPD V+ GS I+ G W   RA  YG+  E+L  FYA+RT+L   +  + +AN VFA  G
Sbjct: 597 VNPDGVVRGSGIFAGGWGAQRAAVYGVPEEKLGEFYAQRTLLKREVLPEHVANAVFALTG 656

Query: 680 GHLSKCTGNILNVDGGVAAAFVR 702
           G L+  TG  + VD GVAAAF+R
Sbjct: 657 GELTHTTGLHVPVDAGVAAAFLR 679


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: 1222
Number of extensions: 44
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: 702
Length of database: 679
Length adjustment: 39
Effective length of query: 663
Effective length of database: 640
Effective search space:   424320
Effective search space used:   424320
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 24 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 2024 update 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