Alignments for a candidate for lctP in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Azohydromonas australica DSM 1124

Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate WP_028997377.1 H537_RS0107285 L-lactate permease

Query= TCDB::Q46839
         (560 letters)



>NCBI__GCF_000430725.1:WP_028997377.1
          Length = 553

 Score =  487 bits (1254), Expect = e-142
 Identities = 261/565 (46%), Positives = 355/565 (62%), Gaps = 20/565 (3%)

Query: 2   VTWTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMP 61
           + W Q+Y P G + +S L+  IP++   VAL  L +K H+A  + L+ + LIA+FA+ MP
Sbjct: 1   MVWQQVYDPFGNMFISTLLGAIPVVVMLVALGFLHIKAHIAAGLGLLAAFLIAVFAYGMP 60

Query: 62  IDMAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLI 121
             MA  AA  G + GL PI WI++  +FL++LT  +G F I++ S+  IT D+RLQ+LLI
Sbjct: 61  ASMAGNAAFLGGLTGLLPIGWIVLNIIFLHQLTEQNGSFKILQDSIAGITQDRRLQLLLI 120

Query: 122 GFSFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAG 181
            F+FGA  EGAAGFG PVA+T A+L+GLGF PL A+GL LIANTAPVA+GALG P++   
Sbjct: 121 AFAFGAFFEGAAGFGTPVAVTAAILIGLGFSPLAASGLSLIANTAPVAYGALGTPVITLA 180

Query: 182 QVTGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFT 241
           QV G D   + AM GRQLPF S+LVPFWL+    G K + E WPA LV G SFA++QFF 
Sbjct: 181 QVHGYDLQEVSAMIGRQLPFFSLLVPFWLIWAFAGRKAMMEIWPAILVTGASFALSQFFV 240

Query: 242 SNYIGPELPDITSALVSIVSLALFLKVWRPKNTETAISM-GQSAGAMVVNKPSSGGPVPS 300
           SNYIGPEL D+ +A+VS+VSL  FL+VW+PK   T++S+ G          P+   PV  
Sbjct: 241 SNYIGPELVDVIAAIVSMVSLVSFLRVWKPKTIWTSVSLKGHDKDGGEAKAPA---PV-V 296

Query: 301 EYSLGQIIRAWSPFLILTVLVTIWTM----KPFKALFAPGGAFYSLVINFQIPHLHQQVL 356
           ++    +IRAW P+ ILT+ V IW +    K +  ++AP          F I  LH  + 
Sbjct: 297 KHPTADVIRAWLPWAILTLFVFIWGLPEVKKFWNGIYAP---------KFPIAGLHNLIE 347

Query: 357 KAAPIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFILGVGIKKGIGVFAETLISLKWP 416
           K  P+V  P    A++ F+ LSA GT I +AAI+    +       +  F  TL  +++ 
Sbjct: 348 KVPPVVPTPHKEAAIYTFNLLSATGTGILLAAIVGGLAMKYNPVALVKTFFRTLWLVRYS 407

Query: 417 ILSIGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFG 476
           +L+I ++LA   +T +SG  TTL L  A TG M+PFF   +GWLGV LTGSDT+SN LFG
Sbjct: 408 LLTIVLMLALGTLTRFSGTDTTLGLAFANTGWMYPFFGTLMGWLGVALTGSDTASNVLFG 467

Query: 477 SLQSTTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHS 536
            +Q   A+Q+ +S  L+ AAN+SGGV GKMI  QSI VA  AT     E ++ RY   HS
Sbjct: 468 GMQKVAAEQLGLSANLMGAANSSGGVMGKMIDAQSIVVASTATRWFNHEGDILRYVFFHS 527

Query: 537 LIFASVIGIITLLQAYV--FTGMLV 559
           +  A ++GI   +QAYV  FT M++
Sbjct: 528 VALACLVGIFVTMQAYVWPFTLMVI 552


Lambda     K      H
   0.327    0.141    0.424 

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: 955
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: 560
Length of database: 553
Length adjustment: 36
Effective length of query: 524
Effective length of database: 517
Effective search space:   270908
Effective search space used:   270908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 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 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