Alignments for a candidate for lctP in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for lctP in Cupriavidus basilensis 4G11

Align L-lactate permease (characterized, see rationale)
to candidate RR42_RS21280 RR42_RS21280 L-lactate permease

Query= uniprot:Q8EIL2
         (545 letters)



>FitnessBrowser__Cup4G11:RR42_RS21280
          Length = 580

 Score =  744 bits (1921), Expect = 0.0
 Identities = 384/571 (67%), Positives = 454/571 (79%), Gaps = 37/571 (6%)

Query: 3   WTQTYTPLGSLWLTAIVALLPIVFFFLALTVLKLKGHIAGALTLLIALAVAIITYKMPVS 62
           WTQTYTPLGSLWL+A+ A LPI+FFFLAL VL++KGH+A A+TLL+AL VAI  Y MPV 
Sbjct: 4   WTQTYTPLGSLWLSALAAALPILFFFLALAVLRMKGHVAAAITLLLALGVAIFAYGMPVP 63

Query: 63  IALASAIYGFSYGLWPIAWIIITAVFLYKITVKTGQFEIIRSSVISVTEDQRLQMLLVGF 122
            ALA+A +GF+YGLWPIAWII+TAVFLYKI VKTGQF+IIR+SV+++T+DQRLQMLL+GF
Sbjct: 64  QALAAAGFGFAYGLWPIAWIIVTAVFLYKIVVKTGQFDIIRASVLAITDDQRLQMLLIGF 123

Query: 123 SFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 182
           +FGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV
Sbjct: 124 AFGAFLEGAAGFGAPVAITAALLVGLGFNPLYAAGLCLIANTAPVAFGAMGIPIIVAGQV 183

Query: 183 SSLDPFHIGQLAGRQLPILSIIVPFWLIAMMDGIRGIRQTWPATLVAGVSFAVTQFLTSN 242
           + +D  HIG +AGRQLP+LS+ VPFWL+ +MDG RG+++TWPA LV G SF+VTQ+ TSN
Sbjct: 184 TGIDAMHIGAMAGRQLPLLSLAVPFWLVFIMDGKRGVKETWPAALVTGASFSVTQYFTSN 243

Query: 243 FIGPELPDITSALVSLICLTLFLKVWQPKEIFTFSGMKQRA--------------VTPKS 288
            IGPELPDITSALVSL+ LTLFLKVWQPK     +G   +A               +   
Sbjct: 244 HIGPELPDITSALVSLVSLTLFLKVWQPKSASQRAGGAVKAGGGAAALARMGGGLASDAG 303

Query: 289 TFSNG-----------------QIFKAWSPFIILTAIVTLWSIKDVQL------ALSFAT 325
           +F NG                 Q  +AW+PF ILTAIVT+WS+   +       AL+   
Sbjct: 304 SFGNGAGDGAGNNRRASPYTVAQTVRAWAPFGILTAIVTVWSLPSFKALFVGNGALAGWV 363

Query: 326 ISIEVPYLHNLVIKTAPIVAKETPYAAIYKLNLLGAVGTAILIAAMISIVVLKMSISNAL 385
           +   VP L  LVIK APIVA+   Y A++KL+L+ AVGTAIL+ A+IS V+L+M    AL
Sbjct: 364 LKFHVPALDQLVIKAAPIVAQPKAYEAVFKLDLVSAVGTAILLTALISAVLLRMKPGAAL 423

Query: 386 TSFKDTLIELRFPILSIGLVLAFAFVANYSGLSSTLALVLAGTGVAFPFFSPFLGWLGVF 445
            +F +TL+ELR PILSIGLVL FAFVANYSG+SSTLAL+LAGTG AFPFFSPFLGWLGVF
Sbjct: 424 ATFGETLMELRRPILSIGLVLGFAFVANYSGMSSTLALLLAGTGAAFPFFSPFLGWLGVF 483

Query: 446 LTGSDTSSNALFGALQANTANQIGVTPELLVAANTTGGVTGKMISPQSIAVACAATGLAG 505
           LTGSDTSSNALF +LQ+ TA+QIGV+  LLVAANTTGGVTGKMISPQSIAVACAATGL G
Sbjct: 484 LTGSDTSSNALFCSLQSTTAHQIGVSDTLLVAANTTGGVTGKMISPQSIAVACAATGLVG 543

Query: 506 KESDLFRFTLKHSLFFCTFIGVLTVLQAYIV 536
           KES+LFRFT+KHSL F   +G++T+LQAY++
Sbjct: 544 KESELFRFTVKHSLLFAMIVGIITMLQAYVL 574


Lambda     K      H
   0.327    0.140    0.419 

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: 1035
Number of extensions: 32
Number of successful extensions: 3
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: 545
Length of database: 580
Length adjustment: 36
Effective length of query: 509
Effective length of database: 544
Effective search space:   276896
Effective search space used:   276896
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 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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