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

GapMind for catabolism of small carbon sources

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

Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate CA265_RS16770 CA265_RS16770 GMC family oxidoreductase

Query= reanno::Cola:Echvi_1847
         (559 letters)



>FitnessBrowser__Pedo557:CA265_RS16770
          Length = 578

 Score =  243 bits (619), Expect = 2e-68
 Identities = 195/589 (33%), Positives = 277/589 (47%), Gaps = 58/589 (9%)

Query: 6   YDAIVVGSGISGGWAAKELTEKGLKVLLLERGQNVEHVKDYKNATLPPWEIPHRGRRTTE 65
           YDAI+VGSG  GG AA  L   G KVLLLE GQN +   D      P WE P RG  TT 
Sbjct: 13  YDAIIVGSGAGGGMAAYVLAHAGQKVLLLEAGQNFDPRLDSHQLKWP-WESPRRGASTT- 70

Query: 66  MVENHPNLKRDYVLNELVLDWWAHEDTSPYVEEKP--FTWFRGYQVGGRSLLWGRQSYRW 123
                    R +   +     W  E   PY ++    F WFR   +GGR+  WGR S R 
Sbjct: 71  ---------RPFGDFDASYGGWELEG-EPYTQKNKSEFEWFRSRMLGGRTNHWGRISLRM 120

Query: 124 SDLDFEANLKEGIAVDWPIRYKDIAPWYDYVEKFAGIAGNRDGLDVLPDGEFMPPFAMNC 183
              DF+   K+G+   WPI Y D+ P+YD V++  GI G  +GL+  PDG FM P     
Sbjct: 121 GPEDFKP--KDGLTDAWPITYADVKPFYDKVDRMIGIYGTAEGLENEPDGIFMKPPKPRL 178

Query: 184 VEKDVKERIAKHFEGKRHLINSRVANITEPLPG---RPGCQARNKCWLGCPFGGYFSTQA 240
            E  +K+   K       +I  R + +TE LP    R  C    +C   C   G FS+ +
Sbjct: 179 NELFIKKGAEK---AGVKVITGRGSVLTEALPNNNDRAPCFYCGQCGRSCKVYGDFSSSS 235

Query: 241 STLPAAMATGNLTLRPYSIVHRVLYDKDTKKATGVEIVDAETMETIEYKSKIVFLCASAL 300
             +  A+ TGNLT+   ++V  V+ DKD   A GV  V+ + ++  +   K+V L ASA 
Sbjct: 236 CLVNPAVKTGNLTVITDAMVREVITDKDGS-AKGVSYVNRKDLQEYQVNGKLVILGASAC 294

Query: 301 NSAHVLMRSATDIWPEGLGSSSGELGHNVMDHHFRLGASGTVEGY-----DDKYYFGRRP 355
            SA +L+ S +   P GL +SSG +G  +   H   GAS  V G+     D K Y     
Sbjct: 295 ESARILLNSKSTSHPNGLANSSGVVGKYL---HDSTGAS--VSGFLPQLMDRKRYNEDGL 349

Query: 356 GGIYIPRYRNVGDDKRDYVRGFG--YQGGASRS--GWGRDVAEMNIGGPMKEA-LTEPGP 410
           G ++I     + + K ++ RG+   Y GG      G+G  VA+MN   P ++  + E G 
Sbjct: 350 GSVHIYSPWWLDNRKLNFPRGYHIEYWGGMGMPAYGFGGGVAQMNGMVPGRDGKMKEAGG 409

Query: 411 WS--------------MGMMAFGEILPYHENTIKISKDVKDKWGMYALVMNAEIKDNEQK 456
           +               +GM   G  +   +N  +I  +  DK+G+  L  N +   +E  
Sbjct: 410 YGKSLKDDYRRFYGTGVGMAGRGTAIAREDNYCEIDPNTVDKYGIPVLRFNYKWAKDEIL 469

Query: 457 MRKDMMNDAAEMLEAAGV---KNIHTYDSGYTF---GQGIHEMGTARMGRDPKTSVLNEN 510
             K M      +++  G      I   D+ Y     G+ IHE+GT RMG DPK S LN+ 
Sbjct: 470 QAKHMQETFLSIMKEMGAVVTSEIQGADTNYGLLNPGKIIHEVGTIRMGDDPKKSALNKY 529

Query: 511 NQVWDAKNVFVTDGAAMTSAAAVNPSLTYMALTARAADFAVKELKKGNL 559
            Q  D KN+FV D          N + T +AL+ R A++ + + KK N+
Sbjct: 530 CQAHDCKNLFVVDAGPFVQQGDKNATWTILALSMRTAEYILAQKKKQNI 578


Lambda     K      H
   0.317    0.135    0.421 

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: 855
Number of extensions: 59
Number of successful extensions: 9
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: 559
Length of database: 578
Length adjustment: 36
Effective length of query: 523
Effective length of database: 542
Effective search space:   283466
Effective search space used:   283466
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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