GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Pantoea rwandensis LMG 26275

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_084933101.1 HA51_RS05940 dipeptide ABC transporter ATP-binding protein

Query= TCDB::Q9X271
         (324 letters)



>NCBI__GCF_002095475.1:WP_084933101.1
          Length = 328

 Score =  292 bits (747), Expect = 9e-84
 Identities = 153/316 (48%), Positives = 211/316 (66%), Gaps = 1/316 (0%)

Query: 2   MELLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRN 61
           M LLNV  L V F   +   +AVD ISY++ +G+ +GIVGESGSGKSVS L+++ LI+  
Sbjct: 1   MALLNVEKLSVHFGDEKTPFRAVDRISYQVEQGQVVGIVGESGSGKSVSSLAIMGLIDYP 60

Query: 62  GRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHR 121
           GR++  +  F  +DL K++++E R + G ++++IFQ+PMTSLNP   VG Q+ME +  H+
Sbjct: 61  GRVMAEKLEFNQRDLQKISEKERRQLVGAEVAMIFQDPMTSLNPCYTVGFQIMEALKVHQ 120

Query: 122 LMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEP 181
                  R+RAI+LL++VGIP+   R   YP Q SGGM QRVMIAMA+AC PKLLIADEP
Sbjct: 121 GGSKSTRRQRAIDLLDQVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACKPKLLIADEP 180

Query: 182 TTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEE 241
           TTALDVTIQAQI+ELL +L+++  M++I ITHDL++       II MYAG++VE     +
Sbjct: 181 TTALDVTIQAQIIELLLDLQKQENMALILITHDLALVAEAAQHIIVMYAGQVVETGKAVD 240

Query: 242 ILKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQRE 301
           I K P HPYT+ +L +  E  +   +L  +PG  P     P+GC  +PRC +  E C+RE
Sbjct: 241 IFKAPRHPYTQAMLRALPEFAADKARLASLPGVVPGKYDRPTGCLLNPRCPYVTERCRRE 300

Query: 302 EPPLVNISENHRVACH 317
           EP L +I    +  CH
Sbjct: 301 EPELRDI-PGRQSKCH 315


Lambda     K      H
   0.320    0.139    0.401 

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: 263
Number of extensions: 7
Number of successful extensions: 1
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: 324
Length of database: 328
Length adjustment: 28
Effective length of query: 296
Effective length of database: 300
Effective search space:    88800
Effective search space used:    88800
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: 48 (23.1 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