Alignments for a candidate for lctP in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Methylobacterium nodulans ORS 2060

Align Glycolate permease, GlcA or YghK (substrates: L-lactate, D-lactate and glycolate) (characterized)
to candidate WP_015933366.1 MNOD_RS33350 L-lactate permease

Query= TCDB::Q46839
         (560 letters)



>NCBI__GCF_000022085.1:WP_015933366.1
          Length = 559

 Score =  509 bits (1310), Expect = e-148
 Identities = 265/562 (47%), Positives = 362/562 (64%), Gaps = 11/562 (1%)

Query: 4   WTQMYMPMGGLGLSALVALIPIIFFFVALAVLRLKGHVAGAITLILSILIAIFAFKMPID 63
           W Q+Y P G   LS + A +P++     +A  ++K HVA  I L+++  +A   F MP  
Sbjct: 2   WNQVYDPFGNAWLSTIAAAVPVVALLALIASGKVKAHVAAVIALVIAFAVATVLFGMPTG 61

Query: 64  MAFAAAGYGFIYGLWPIAWIIVAAVFLYKLTVASGQFDIIRSSVISITDDQRLQVLLIGF 123
           +A  AAG G   GL+PIAWII+  +FLY+LTV  G F  ++ SV  IT D+RLQ+LL+ F
Sbjct: 62  LALRAAGLGIATGLFPIAWIILNVIFLYRLTVEKGWFATLQQSVAGITADRRLQLLLVAF 121

Query: 124 SFGALLEGAAGFGAPVAITGALLVGLGFKPLYAAGLCLIANTAPVAFGALGVPILVAGQV 183
           +FGA  EGA GFG PVA+TGA+L+GLGF PL A+GL LIANTAPVA+GALG PI     V
Sbjct: 122 AFGAFFEGAGGFGTPVAVTGAILIGLGFSPLAASGLSLIANTAPVAYGALGAPIQGLASV 181

Query: 184 TGIDPFHIGAMAGRQLPFLSVLVPFWLVAMMDGWKGVKETWPAALVAGGSFAVTQFFTSN 243
           TG DP+ +GAM GRQLPF S+LVPFWL+ +  G++G+ + WPA LV G SFA  QF  SN
Sbjct: 182 TGYDPYLLGAMIGRQLPFFSLLVPFWLIVVFAGFRGMAQIWPAVLVCGASFAAAQFLISN 241

Query: 244 YIGPELPDITSALVSIVSLALFLKVWRPKN--TETAISMGQSAGAMVVNKPSSGGPVPSE 301
           Y+ P + DI ++LVS+ +L  FL+VW P    T TA+     + A    +P+S G   +E
Sbjct: 242 YVNPWIVDIGASLVSMGALVAFLRVWHPAQIWTSTALRTHDDSMAYAPPRPASLGAAAAE 301

Query: 302 YSLGQ--IIRAWSPFLILTVLVTIWTMKPFKALFAPGGAFYSLVINFQIPHLHQQVLKAA 359
            +  Q  I+ AW P++IL+V+V IW    FK L  P          +++  LH  V+K  
Sbjct: 302 RTATQREILMAWVPWIILSVIVAIWGTGWFKNLVNP-----LFTWRYEVEGLHNLVMKVP 356

Query: 360 PIVAQPTPMDAVFKFDPLSAGGTAIFIAAIISIFILGVGIKKGIGVFAETLISLKWPILS 419
           P+VA+  P  AVF F  +S  GT +  AAIIS  I+G G  + +  + ET+  L++ I +
Sbjct: 357 PVVAKAHPEPAVFLFTYMSFTGTGVLFAAIISGLIMGFGPIRLVRAYLETIWVLRYSITT 416

Query: 420 IGMVLAFAFVTNYSGMSTTLALVLAGTGVMFPFFSPFLGWLGVFLTGSDTSSNALFGSLQ 479
           I  +LA   +T Y+G+  TL L  AGTG+++PFF   LGWLGV LTGSDT+SN LFG LQ
Sbjct: 417 IAAMLAIGVLTRYAGVDATLGLAFAGTGLLYPFFGTLLGWLGVALTGSDTASNVLFGGLQ 476

Query: 480 STTAQQINVSDTLLVAANTSGGVTGKMISPQSIAVACAATGMVGRESELFRYTVKHSLIF 539
             T++Q+ +S  L+ AAN+SGGV GKMI  QSI VA  ATG  G+ES++ R+   HS++ 
Sbjct: 477 RITSEQLGLSGILMAAANSSGGVMGKMIDAQSIVVASTATGYFGQESKILRFVFWHSIVL 536

Query: 540 ASVIGIITLLQAYV--FTGMLV 559
           A ++G + +LQAYV  FT ++V
Sbjct: 537 ACLVGGLVMLQAYVPPFTSLVV 558


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: 984
Number of extensions: 44
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: 559
Length adjustment: 36
Effective length of query: 524
Effective length of database: 523
Effective search space:   274052
Effective search space used:   274052
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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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