GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Paraburkholderia bryophila 376MFSha3.1

Align Inositol transport system ATP-binding protein (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= reanno::Phaeo:GFF717
         (261 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  168 bits (426), Expect = 2e-46
 Identities = 90/240 (37%), Positives = 144/240 (60%), Gaps = 5/240 (2%)

Query: 7   LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66
           +++++G+ K F  V+AL G+ +D+  GE H + G+NGAGKST +K +SG +    G I +
Sbjct: 22  ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81

Query: 67  EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126
           EG+P+ FA   DA AAGIA +HQ L ++P +SV+ N ++  EP  K GP    D+   N 
Sbjct: 82  EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREP--KRGP--FVDYRTLNA 137

Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186
                ++++G+N+  P   VG LS  ++Q V IA+A+   A+VLI+DEPTS+L   +T  
Sbjct: 138 NAQRCLQRIGLNV-SPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQ 196

Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246
           +   I ++R  GVA+++I+H +     + DR TVL  G+ + T+     +  E+   M G
Sbjct: 197 LFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVG 256



 Score = 80.1 bits (196), Expect = 9e-20
 Identities = 58/224 (25%), Positives = 96/224 (42%), Gaps = 5/224 (2%)

Query: 26  VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPLHFADPRDAIAAGIA 85
           +S D+  GE     G  GAG++   + + G  +   G I     P+    PR+AI  GIA
Sbjct: 290 LSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIA 349

Query: 86  TVHQHLAMIPL---MSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINLRGP 142
            + +      L   M V+ N  + N  +R I             I    +R++ I     
Sbjct: 350 YLSEDRKKDGLALSMPVAANITLSN--VRAISSRGFLRFSEETAIAERYVRELAIRTPTV 407

Query: 143 DQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATIDKVRKQGVAVV 202
            Q    LSGG +Q + I++ ++ G+++L  DEPT  + V     +   +D++   GV VV
Sbjct: 408 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVV 467

Query: 203 FITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMAG 246
            I+  +   L + DR  V + G      +    S EE+    +G
Sbjct: 468 LISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYASG 511


Lambda     K      H
   0.321    0.137    0.395 

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: 298
Number of extensions: 13
Number of successful extensions: 4
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: 261
Length of database: 515
Length adjustment: 30
Effective length of query: 231
Effective length of database: 485
Effective search space:   112035
Effective search space used:   112035
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 (21.9 bits)
S2: 49 (23.5 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