Alignments for a candidate for aldA in Streptacidiphilus oryzae TH49

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Streptacidiphilus oryzae TH49

Align Lactaldehyde dehydrogenase (EC 1.2.1.22); Rhamnulose-1-phosphate aldolase (EC 4.1.2.19) (characterized)
to candidate WP_037571372.1 BS73_RS10620 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

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



>NCBI__GCF_000744815.1:WP_037571372.1
          Length = 687

 Score =  664 bits (1713), Expect = 0.0
 Identities = 350/685 (51%), Positives = 450/685 (65%), Gaps = 18/685 (2%)

Query: 28  VALLIYRSNILGADLRITNYGGGNTSCKTTEVDPLTKEETEVMWVKGSGGDIGTLKRSGL 87
           V  L+ RS+ LG+D R TNY GGNTS K T  DP+T  E E++WVKGSGGD+GTL  SGL
Sbjct: 11  VRALLERSHRLGSDPRNTNYAGGNTSAKGTGTDPVTGREVELLWVKGSGGDLGTLGESGL 70

Query: 88  AGLYVEKLHSLKNVYRGLEFEDEMVGLFNHCIYDLDSKAPSIDTPLHAFLPFKHIDHLHP 147
           A L +++L SL +VY G++ EDEMV  F+ C++     APSIDT +HA +   H+DHLHP
Sbjct: 71  AVLRLDRLRSLADVYPGVDREDEMVAAFDFCLHGRGGAAPSIDTAMHALVDAPHVDHLHP 130

Query: 148 DAAIAIAASKDGEKITEELFEGQIAWVPWQRPGFDLALQLEKALNENPGIRGIMLGGHGL 207
           D+ IA+A + DGEK+T E F   + WVPW+RPGF L L +      NP   G +LGGHG+
Sbjct: 131 DSGIALATAADGEKLTAECFGDTVVWVPWRRPGFQLGLDIAAIKEANPQAVGCVLGGHGI 190

Query: 208 FTWGDTAYECYINSLEVIDKASEYLE---QNYGKDRPVFGG--QKIESLAPEQRQEQASI 262
             WG T+ E   NSL +I  A  ++E   +  G+  P FG       +L   +R+E+A+ 
Sbjct: 191 TAWGATSEEAEANSLHMIRTAERFIEAKGREGGRAEP-FGPLLDGYGALPEAERRERAAA 249

Query: 263 IAPVLRGLASGYNRMVGHFTDDERVLQFANSHDLEKLAPLGTSCPDHFLRTKIRPLVLDF 322
           +AP++RGLAS     VGHFTD E VL F    +  +LA LGTSCPDHFLRTK+RPLVLD 
Sbjct: 250 LAPLIRGLASTDRPQVGHFTDAEPVLDFLARAEHPRLAALGTSCPDHFLRTKVRPLVLDL 309

Query: 323 PADVDLSKADEIKEKLDKDFEEYRAYYKKYYEDHKRDNSPAMRDPNPVVIIWPGVGMFSY 382
           PAD  L  A    E+L      YR  Y+ YY+ H   +SPAMR  +P +++ PGVGMFS+
Sbjct: 310 PADAPLEAA---VERLKALHSAYREEYRAYYDRHADADSPAMRGADPAIVLVPGVGMFSF 366

Query: 383 AKNKQTARVASEFYINAINVMRGAEAVSEYVALPLQEAFDIEYWLLEEAKLQRMPKEQPL 442
            K+KQTARVA EFY+NA+NVMRGAE VS Y  +   E F IEYW LEEAKLQRMPK +PL
Sbjct: 367 GKDKQTARVAGEFYLNAVNVMRGAETVSTYAPIEESEKFRIEYWALEEAKLQRMPKPKPL 426

Query: 443 SRKVALVTGGAGGIGKAIADKLASEGACVFITDINQERLDGAVATYSKDVGG-----GAV 497
           + +VALVTG A GIG+AIA++L +EGACV + D+N E    A    ++ +GG        
Sbjct: 427 ATRVALVTGAASGIGRAIAERLVAEGACVVVADLNAE----AAGVVAEQLGGPDKAVAVT 482

Query: 498 MDVTKGDDIIKAYKAAALKFGGVDIIVNCAGLAISKPIEQTSEQDWDLLQDILVKGQFAV 557
           +DVT    I +A++AAAL FGGVD++VN AG++ISKP+ +T+  DWDL   I+ +G F V
Sbjct: 483 VDVTDEAQIAEAFRAAALAFGGVDLVVNNAGISISKPLLETTAGDWDLQHAIMARGSFLV 542

Query: 558 SKAGVETLRAQNLGGDIINIASKNALVSGPNNVGYGTAKAAQVHMSRLLAAELGKDKIRV 617
           S+     +  Q LGGDI+ IASKN++ +GPNN+ Y   KA Q H  RLLAAELG+  IRV
Sbjct: 543 SREAARMMAEQGLGGDIVYIASKNSVFAGPNNIAYSATKADQAHQVRLLAAELGEHGIRV 602

Query: 618 NVVNPDAVIEGSKIWEGEWAKGRAKAYGITVEELPAFYAKRTILNEIIGVDDIANGVFAF 677
           N VNPD V+ GS I+   W   RA  YGI   EL  FYA+RTIL   +  + +AN VFA 
Sbjct: 603 NGVNPDGVVRGSGIFANGWGAQRAATYGIEESELGEFYAQRTILKREVLPEHVANAVFAL 662

Query: 678 VGGHLSKCTGNILNVDGGVAAAFVR 702
            GG L+  TG  + VD GVAAAF+R
Sbjct: 663 TGGELTHTTGLHVPVDAGVAAAFLR 687


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: 1184
Number of extensions: 51
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: 687
Length adjustment: 39
Effective length of query: 663
Effective length of database: 648
Effective search space:   429624
Effective search space used:   429624
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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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