GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Mesorhizobium ciceri WSM1271

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate YP_004141765.1 Mesci_2579 binding-protein-dependent transport system inner membrane protein

Query= TCDB::Q8YPM7
         (381 letters)



>NCBI__GCF_000185905.1:YP_004141765.1
          Length = 359

 Score =  175 bits (444), Expect = 2e-48
 Identities = 121/395 (30%), Positives = 186/395 (47%), Gaps = 69/395 (17%)

Query: 3   KLTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWA-----------------TTKAQW 45
           +L  LR+  F+T   +++++ C  + ++LV  ++ WA                 T  A W
Sbjct: 13  RLEDLRRRFFATPLQAVVSLACLTIMVFLVWKLLNWAVFSAVFTTSGGPEACQATAGACW 72

Query: 46  AVIQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVG 105
           +VI    R+   G +P  E WR        S L  V                        
Sbjct: 73  SVIAARWRIIFFGLYPYEEQWR--------SALACVAV---------------------- 102

Query: 106 LLLILFTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLIGGGF 165
                          +++T +  IP F  G R+  +      L ++L       + GG  
Sbjct: 103 ---------------VVMTVLSCIPAFWTGRRIALVWGAGTGLFYVL-------MKGGVL 140

Query: 166 GLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVP 225
           GL  V    W GL LTL +   + ++ FP+ + LAL R S LP +   + L I+ VR +P
Sbjct: 141 GLAHVGEEAWGGLALTLFIFVTTCLIGFPLAICLALLRRSELPWISRTTGLIIDGVRSLP 200

Query: 226 LIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAK 285
           LI ILF   V+LP      ++ D++ R I G  LF +AY AE VRGG+Q V+ GQ EAA 
Sbjct: 201 LISILFTFAVVLPFALPQWLQGDKLYRVILGSALFFSAYQAEIVRGGMQGVATGQEEAAM 260

Query: 286 ALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQ 345
           ALG+  +  +  I+LPQA+R  +PA + QF+  FK+TSL+ +VG  E+     +     +
Sbjct: 261 ALGMRYWQRISRILLPQAMRNAMPATINQFVISFKETSLVVIVGFFEILASGNAAYGTGE 320

Query: 346 FIGRYAEVYLFIGLIYWLFCYSMSLASRRLERQLN 380
           +   Y EVY FI  IY++F +S+S     LER+++
Sbjct: 321 WRFAYVEVYAFIAFIYFIFVFSLSRYGAFLERRMS 355


Lambda     K      H
   0.332    0.145    0.452 

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: 430
Number of extensions: 29
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: 381
Length of database: 359
Length adjustment: 30
Effective length of query: 351
Effective length of database: 329
Effective search space:   115479
Effective search space used:   115479
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 49 (23.5 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