Alignments for a candidate for rhaD in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaD in Phyllobacterium brassicacearum STM 196

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_106713916.1 CU102_RS25585 bifunctional rhamnulose-1-phosphate aldolase/short-chain dehydrogenase

Query= reanno::Smeli:SMc02322
         (699 letters)



>NCBI__GCF_003010955.1:WP_106713916.1
          Length = 698

 Score = 1040 bits (2689), Expect = 0.0
 Identities = 513/691 (74%), Positives = 582/691 (84%), Gaps = 1/691 (0%)

Query: 10  LANLWDDGKAAGMTEPEKLLYRSNLLGSDKRITNYGGGNTSAKVMEKDPLTGEIVEVLWV 69
           L N WDD KAAG+ EP KLLYRSNLLG+DKRITNYGGGNTSAK+ E DPLTG  V+VLWV
Sbjct: 8   LDNRWDDQKAAGLDEPGKLLYRSNLLGADKRITNYGGGNTSAKIAETDPLTGRSVDVLWV 67

Query: 70  KGSGGDVGTIKMDGFSTLYMDKLRALKGIYRGVEFEDEMVGYLPHCTFNLNPRAASIDTP 129
           KGSGGDVGTIK+DGF+TLYM+KL++LK IYRGVE ED MVG+LPHCTFNLN RAASIDTP
Sbjct: 68  KGSGGDVGTIKLDGFATLYMEKLQSLKSIYRGVEDEDRMVGFLPHCTFNLNSRAASIDTP 127

Query: 130 LHAYVPKPHVDHMHPDAIIAIAASKNSRELTSKIFGDEIGWLPWKRPGYELGLWLEKFCQ 189
           LH YVP  HVDHMHPDAIIAIAASKNSRELT++IFGD+IGWLPW+RPG++LGL L  +  
Sbjct: 128 LHGYVPFKHVDHMHPDAIIAIAASKNSRELTNEIFGDDIGWLPWRRPGFQLGLDLGAYVA 187

Query: 190 ENPDARGVVLESHGLFTWGDTAKEAYETTIEIINRAIAWFETENTGPA-FGGRSKPVLAA 248
            +P ++GVVLESHGLFTW + AKE YE T+EIIN+AI WF+ + +G + FGG +   L A
Sbjct: 188 AHPKSKGVVLESHGLFTWANDAKECYELTLEIINKAIVWFDQKTSGKSVFGGSTTESLDA 247

Query: 249 ADRAAIAKKLMPVIRGLISAGESKVGHFDDSQAVLDFVTSTSLEPLAALGTSCPDHFLRT 308
           A R  IA +LMP IRG I   E K+GHFDD  AVL+FV S +L PLAALGTSCPDHFLRT
Sbjct: 248 AARRTIAARLMPEIRGKIGVSERKLGHFDDQTAVLEFVNSKALRPLAALGTSCPDHFLRT 307

Query: 309 KIRPLVVDFDPAQPDVGNTLAGLPEAIATYRADYAAYYERCKRADSPAMRDPNAVVYLVP 368
           KIRPLV+DFDPA PD    +A L  A+  YRADYA YY  CK A+SPAMRDPN V++L+P
Sbjct: 308 KIRPLVLDFDPADPDADAVVASLDNALEAYRADYARYYNDCKHANSPAMRDPNPVIFLIP 367

Query: 369 GVGMITFAKDKATARISAEFYVNAINVMRGASGVSTYVGLPEQEAFDIEYWLLEEAKLQR 428
           GVGM++FA+DKATARI+ EFYVNAINVMRGAS VS Y GLPEQEAFDIEYWLLEEAKLQR
Sbjct: 368 GVGMLSFARDKATARIAGEFYVNAINVMRGASSVSEYQGLPEQEAFDIEYWLLEEAKLQR 427

Query: 429 MPKPKSLAGRIALVTGGAGGIGKATANRLMQEGACVVLADIDETALEAAQTELSTRYGKD 488
           MPKPKSLAGR+A VTGGAGGIG+ATA RL+ EGACVVLADID  AL+A   E + RY +D
Sbjct: 428 MPKPKSLAGRVAFVTGGAGGIGRATAERLLGEGACVVLADIDAEALKATYEEFAKRYSED 487

Query: 489 FVRSVNMNVTSEAAVESGFGDALLAFGGLDILVSNAGLATSAAVEDTTLALWNKNMDILA 548
            VRS+ +NVT E AV + + DA + FGG+DILVSNAG+A+SA +E T L++W +NMDILA
Sbjct: 488 AVRSLQLNVTDEVAVIASYADASVEFGGVDILVSNAGIASSAPIETTELSMWTRNMDILA 547

Query: 549 TGYFLVSREAFRIFRNQKAGGNVVFVASKNGLAASPGASAYCTAKAAEIHLARCLALEGA 608
           TGYFLVSREAFR+FR QK GGNVVFVASKNGLAASP ASAYC AKAAEIHLARCLALEGA
Sbjct: 548 TGYFLVSREAFRLFRRQKIGGNVVFVASKNGLAASPNASAYCAAKAAEIHLARCLALEGA 607

Query: 609 SAQIRVNVVNPDAVLRGSKIWTGEWKEQRAAAYKMDVDELEAHYRERSMLKLSVFPEDIA 668
            A IRVN VNPDAVLRGSKIW GEW+EQRAA+  + VDELE HYR+RS+LKL+V PEDIA
Sbjct: 608 EAGIRVNTVNPDAVLRGSKIWNGEWREQRAASSNLQVDELEEHYRKRSLLKLNVLPEDIA 667

Query: 669 EAIYFLASDMSAKSTGNIVNVDAGNAQSFTR 699
           EAIYFLASD SAKSTGNI+NVDAGNAQSFTR
Sbjct: 668 EAIYFLASDASAKSTGNIINVDAGNAQSFTR 698


Lambda     K      H
   0.317    0.133    0.393 

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: 1311
Number of extensions: 37
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: 699
Length of database: 698
Length adjustment: 39
Effective length of query: 660
Effective length of database: 659
Effective search space:   434940
Effective search space used:   434940
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 (21.7 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