GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Marinobacter adhaerens HP15

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Marino:GFF2860
          Length = 672

 Score =  265 bits (677), Expect = 2e-75
 Identities = 133/299 (44%), Positives = 198/299 (66%), Gaps = 5/299 (1%)

Query: 27  KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLND 86
           ++ L+A+D +S+ +K+GE L LVGESGCGK+TL RTI+ L  P  G +   G+ I NL  
Sbjct: 372 RKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGLQAPSTGSVTLNGQRIENLPP 431

Query: 87  KEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIG 146
            +     + +Q IFQDP  SLNP+ T+G II  PL +H IG+ +E+ ++V +++++VG+ 
Sbjct: 432 MDRA---RMIQPIFQDPYSSLNPRKTIGEIIAKPLFVHGIGSNQEQHQQVRKMMELVGLP 488

Query: 147 REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKM 206
               NS+P + SGGQ+QR  I RAL LNP+ ++CDEP SALDVS+QAQI++LL +++ ++
Sbjct: 489 SRVFNSYPDQLSGGQRQRAAIGRALILNPEVVICDEPTSALDVSVQAQILNLLLDLRDEL 548

Query: 207 GISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWD 266
            ++YLF+ HNL+VV+H++ +VAVMYLG+IVE G+ D++  +P HPYT AL+ S   I   
Sbjct: 549 DLTYLFVTHNLSVVQHMADRVAVMYLGEIVECGERDQVMSDPKHPYTHALMNSALSIS-P 607

Query: 267 GQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHLVRS 325
           G+      L G+ P+P++ P GC F  RC      C E+ P   E+  N  V C   R+
Sbjct: 608 GESVPDPGLSGDFPNPMNRPSGCPFHPRCPLADQQCREQAPG-PELIDNTLVQCWKART 665



 Score =  224 bits (572), Expect = 4e-63
 Identities = 123/322 (38%), Positives = 185/322 (57%), Gaps = 9/322 (2%)

Query: 8   IKMKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL 67
           + M  +L   DL    P     L AV GIS+E+  GETLG+VGESG GKS     ++ LL
Sbjct: 1   MNMASILDIQDLSVDIPTDSSTLHAVRGISLELNRGETLGIVGESGSGKSMTALALMNLL 60

Query: 68  RPDGGK----IFFEGKDITNLNDKEM--KPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPL 121
            P   +    I F+G D+T+  ++E+  K   +++ +IFQ+P+ SLNP  ++GR +++ +
Sbjct: 61  PPAAKRQASCIDFDGSDLTHATERELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKETM 120

Query: 122 IIHKIGTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIV 179
            +H+  +  E   R   LL+ VG+      +  +PHE SGGQ+QR+ IA AL   P+ ++
Sbjct: 121 TLHRKVSDTEAENRAVYLLEKVGLPDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLI 180

Query: 180 CDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYG 239
            DEP +ALDV+IQAQI+ LL E+QQ+ G+S + I H+L VV   +  +AVMY G IVE G
Sbjct: 181 ADEPTTALDVTIQAQILHLLRELQQEFGMSMILITHDLGVVSRAADNIAVMYAGDIVETG 240

Query: 240 DVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKK 299
              ++  NP HPYT+ LL+ VP      Q QR  ++ G +P+      GC F +RC    
Sbjct: 241 KTGEVLENPRHPYTKGLLECVPGYKGQSQ-QRLGAIPGIVPAMTGDISGCAFASRCPRAA 299

Query: 300 AICFEKEPELTEVEKNHFVSCH 321
            +C    P   ++ +  +  CH
Sbjct: 300 GVCRTTNPPTKKLHQGRYFVCH 321


Lambda     K      H
   0.321    0.142    0.417 

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: 622
Number of extensions: 24
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 328
Length of database: 672
Length adjustment: 33
Effective length of query: 295
Effective length of database: 639
Effective search space:   188505
Effective search space used:   188505
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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