GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malEIICB in Catellicoccus marimammalium M35/04/3

Align The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized)
to candidate WP_083848942.1 C683_RS02545 PTS transporter subunit EIIC

Query= TCDB::Q63GK8
         (545 letters)



>NCBI__GCF_000313915.1:WP_083848942.1
          Length = 553

 Score =  722 bits (1863), Expect = 0.0
 Identities = 360/550 (65%), Positives = 432/550 (78%), Gaps = 10/550 (1%)

Query: 2   KITSFDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAII 61
           KI SF+FWQKFGKAL+VV+AVMPAAGLMISIGKLI M+   ++   TI  V E+IGWAII
Sbjct: 3   KIFSFEFWQKFGKALMVVIAVMPAAGLMISIGKLIAMA--QVSLAVTIGGVTENIGWAII 60

Query: 62  TNLHILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLA 121
            NL ILFA+AIGGSWAK+RAGGAFA+ LAF+L NRITGA+FGV  EMLA+ +A V ++  
Sbjct: 61  GNLPILFALAIGGSWAKERAGGAFASGLAFILINRITGAVFGVTKEMLANPEATVHTIFG 120

Query: 122 GDLIVKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPF 181
             ++V  YFTSVL APALNMGVFVGII GF GA +YNKYYN+ KLP  L+FFNGKRFVPF
Sbjct: 121 QKILVNGYFTSVLEAPALNMGVFVGIIAGFAGAIIYNKYYNFRKLPNCLSFFNGKRFVPF 180

Query: 182 VVIVWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHH 241
           VVI+WS + A++LS+ WPF Q+G+NEFG+WIA S DSAP  APF+YGTLERLLLPFGLHH
Sbjct: 181 VVILWSVIIALLLSVFWPFAQTGINEFGKWIAQSGDSAPFWAPFIYGTLERLLLPFGLHH 240

Query: 242 MLTIPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNV 301
           MLTIPMNYT+LGGTY +LTG++ GQ V GQDPLWLAW+TDL NL   GD   Y+ LL ++
Sbjct: 241 MLTIPMNYTDLGGTYHILTGAQAGQAVLGQDPLWLAWVTDLINLKEKGDMTQYHQLLESI 300

Query: 302 VPARFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMF 361
            PARFK GQ+IGS+  LMG+ FAM+RNV+ +++  YK +FLSAALAVFLTGVTEP+EFMF
Sbjct: 301 RPARFKVGQMIGSSGILMGVTFAMYRNVEPKRKKVYKQIFLSAALAVFLTGVTEPLEFMF 360

Query: 362 MFIAPVLYVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVS 421
           MF    LYVVYA+  G+AF LAD+I+LR+HAFG IEL+TR PM + AGL  D+INF+I  
Sbjct: 361 MFAGIPLYVVYALLQGVAFGLADIIDLRLHAFGNIELLTRLPMSIKAGLGMDIINFIITC 420

Query: 422 LVFFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDE--------ASEGTGNVQDGSLATKV 473
           +VFF L + + NF+IKKF++ TPGR GNYI+  D+        A+  T   +  +    +
Sbjct: 421 IVFFFLAYFVANFMIKKFHIATPGRLGNYIEGNDDSSASDTTTATSSTKPSEANNQVMNI 480

Query: 474 IDLLGGKENIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKAD 533
           I LLGGKENI DVDACMTRLRVTVKD   VA E  WK+ GA+GLI K+ GVQAVYGPKAD
Sbjct: 481 IQLLGGKENIVDVDACMTRLRVTVKDTTKVADEEAWKKEGAMGLIHKNNGVQAVYGPKAD 540

Query: 534 VLKSDIQDML 543
           VLKSDI D L
Sbjct: 541 VLKSDINDYL 550


Lambda     K      H
   0.325    0.140    0.416 

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: 879
Number of extensions: 39
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: 545
Length of database: 553
Length adjustment: 36
Effective length of query: 509
Effective length of database: 517
Effective search space:   263153
Effective search space used:   263153
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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:

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:

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:

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:

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