GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1746 in Rhodobacter johrii JA192

Align TM1746, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_069331338.1 C8J29_RS19500 peptide ABC transporter substrate-binding protein

Query= TCDB::Q9X268
         (642 letters)



>NCBI__GCF_003046325.1:WP_069331338.1
          Length = 529

 Score =  162 bits (409), Expect = 5e-44
 Identities = 115/368 (31%), Positives = 183/368 (49%), Gaps = 22/368 (5%)

Query: 49  IFEGLFGYVPDPKSLGGVKVVPAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEF 108
           ++EGL   V D ++    KVVP V ES+ +SEDGLTYTF LR D +WSNGDPV A DF F
Sbjct: 57  LYEGLV--VQDAQA----KVVPGVAESWEISEDGLTYTFKLRDDAKWSNGDPVVAEDFVF 110

Query: 109 AWKRAASPETPTLPLWASPVQYIKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSF 168
           A +R  +P T  +  +A+ +  I N     +G K  +ELGV+A+D++TL+ TL+ P P F
Sbjct: 111 ALRRIMTPATAAI--YANILYPIANAEAVATGGKQPEELGVEAVDEHTLKFTLNAPTPYF 168

Query: 169 INMLVLGGAMPLHRKTVQEHPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGDFP 228
           + +L    ++P+HR TV+    ++ KP   V NG Y + SF PN  IV+ +N+++     
Sbjct: 169 LELLTHQSSLPMHRATVEAEGSNFTKPGVMVTNGAYKLVSFAPNDRIVMEKNEHFHDAAN 228

Query: 229 GNVDR---IVLKAGGLGLQQYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQWVG 285
             +DR   +  +     L+++ A E+     T V     A   + L  ELH    +    
Sbjct: 229 VAIDRVEWVPFEDRSACLRRFEADEVQ--MCTDVPAEQMAYMRENLKDELHVAPYLGTYY 286

Query: 286 YEITRSLSPVFDDIRIRKALAMAIDKKVLTDIVLGGMAIPTHAYCSPD-SEIAEAVKGIP 344
             +  +      D R+R+A++M +D+  + + V     +P ++   P  S   E    + 
Sbjct: 287 LPVKGADGSPLKDKRVRQAISMVLDRDFIAEEVWQETMLPGYSMVPPGISNYVETPPALD 346

Query: 345 YDPE-------QAKKLLAEAGYPNGKGFPKVKFYITGASDPVAEALVDQWKKVLGITFEI 397
           Y  E       +AK LL EAG   G    ++ +  +        A+ D  K + GI   +
Sbjct: 347 YADEDLLDREDKAKALLEEAGVAEGSLTVQLSYNSSENHRNTMTAIADMLKNI-GINATL 405

Query: 398 ENIESGQF 405
             +E   +
Sbjct: 406 NEMEGTNY 413


Lambda     K      H
   0.319    0.138    0.431 

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: 812
Number of extensions: 39
Number of successful extensions: 2
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: 642
Length of database: 529
Length adjustment: 36
Effective length of query: 606
Effective length of database: 493
Effective search space:   298758
Effective search space used:   298758
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 (21.7 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:

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