GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Mesorhizobium ciceri WSM1271

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate YP_004141766.1 Mesci_2580 binding-protein-dependent transport system inner membrane protein

Query= CharProtDB::CH_011913
         (426 letters)



>NCBI__GCF_000185905.1:YP_004141766.1
          Length = 387

 Score =  176 bits (446), Expect = 1e-48
 Identities = 127/417 (30%), Positives = 217/417 (52%), Gaps = 48/417 (11%)

Query: 17  LIYDTRFRSITIQIV----VLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLA 72
           L+ + + R+  +Q++    +  + LAG+V     A  NL  +G    F FL+   G+D+ 
Sbjct: 4   LLRNQKVRNALLQVLYVGSIAAMVLAGIVI----ARRNLADQGITSGFDFLFKSTGWDVN 59

Query: 73  QTLIPYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYV 132
            +L+P + +D ++   + G++NTL +  +G ILATI+GTI+G+ R S N L   +   YV
Sbjct: 60  FSLLPATANDPYWWYFLIGIINTLFLGSVGLILATIVGTIVGLARTSSNDLARLLGRTYV 119

Query: 133 ETFRNIPLLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTN 192
           + FRNIPL+L +     I+    P P+                   W F    +T+RG  
Sbjct: 120 DIFRNIPLILQVFFWYAIITHL-PTPRSAH--------------EAWGF---LLTSRGLY 161

Query: 193 LPAPAFDHSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTW 252
           +P P             N+  +  A A +AV++A       ++ R   + +  G R T  
Sbjct: 162 IPFP-------------NVGSAAFAAATVAVIAAIVLP--AWLGRTSLLAQPIGQRRTIQ 206

Query: 253 WPSLLILFAPISALLYGLGFH-----LDYPQITKFDFTGGFQMLHSFTALLIALTLYTAA 307
           + +     A  + ++  LG       LD+P +   +  GG ++   F  L IA+ +Y  +
Sbjct: 207 FAAAAAALA-CATIILALGRLPDTPLLDFPALQGLNLRGGLRIPPEFATLAIAIAIYGGS 265

Query: 308 FIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSS 367
           +IAEIVR G +++  GQ EAA +LGL P R  +LV LP ALR ++P L +Q++ L K ++
Sbjct: 266 YIAEIVRGGFKSVGTGQVEAALSLGLSPWRVFTLVRLPLALRAMLPILANQYVWLMKATT 325

Query: 368 LAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLK 424
           + IAV + D    +  +T+N +G+ LE + ++M  +L I+L+++++ N  NK+I LK
Sbjct: 326 MGIAVGFTDF-FMIVALTINHSGQTLEAIGILMAGFLAINLSLAAVFNRINKAIALK 381


Lambda     K      H
   0.326    0.139    0.419 

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: 337
Number of extensions: 17
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: 426
Length of database: 387
Length adjustment: 31
Effective length of query: 395
Effective length of database: 356
Effective search space:   140620
Effective search space used:   140620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 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