GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaD 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:

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:

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