GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Paraburkholderia bryophila 376MFSha3.1

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  442 bits (1138), Expect = e-128
 Identities = 237/493 (48%), Positives = 324/493 (65%), Gaps = 2/493 (0%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86
           +L++  VSK FPGVVAL  + L +R G V A+ GENGAGKSTLMKII+G Y  D G +  
Sbjct: 22  ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81

Query: 87  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146
            GKPV F +   A  AGIA+IHQELNL+PH+S+AENI++ RE   G   +D+R ++    
Sbjct: 82  EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRG-PFVDYRTLNANAQ 140

Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206
           + L+R+ +N+ P   VG LSIA++QMVEIAKA+S D+ +LIMDEPTS++T+ E   LF I
Sbjct: 141 RCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRI 200

Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266
           I +L+A G  I+YI+H+++E+  I D V V RDG +I      S   + +++ MVGR L 
Sbjct: 201 IRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRALD 260

Query: 267 QLFPVREK-PIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 325
             +P RE  P   +LM VRDL+    F  +SFDL  GEILG AGLMG+GRT VA AIFG 
Sbjct: 261 DAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIFGA 320

Query: 326 TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAG 385
              D G I L   PV I  P  AI  G A L+EDRK  GL   + V  N+ ++ +   + 
Sbjct: 321 ERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAISS 380

Query: 386 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 445
            GF++     A+ E   ++L ++TP+++Q    LSGGNQQK ++++WL    RIL  DEP
Sbjct: 381 RGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDEP 440

Query: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505
           TRGIDVGAK  IY+L+  LA++G+ V++ISSELPE+LGM+DR+ V HEG +   L+  + 
Sbjct: 441 TRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETRQT 500

Query: 506 TQERVMQLASGMS 518
           +QE ++  ASG S
Sbjct: 501 SQEEILHYASGRS 513



 Score =  102 bits (253), Expect = 4e-26
 Identities = 69/243 (28%), Positives = 123/243 (50%), Gaps = 15/243 (6%)

Query: 286 LRLDGVFK---------GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLD 336
           L+L GV K         G+  DL +GE+  + G  G+G++ + + I G   +D G IC +
Sbjct: 23  LQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICYE 82

Query: 337 GQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRA 396
           G+PV+ +    A   G A++ ++  L    P LSV EN+ +A  P      F+  + L A
Sbjct: 83  GKPVQFASTSDAQAAGIAIIHQELNL---VPHLSVAENIYLAREPKRGP--FVDYRTLNA 137

Query: 397 LCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAE 456
             +   +++ +   S    +  LS   QQ   +A+ L  + R+LI+DEPT  +      +
Sbjct: 138 NAQRCLQRIGLNV-SPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQ 196

Query: 457 IYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516
           ++R+I  L ++G+A++ IS  L E+  + DRV V+ +G  + T D +  T   ++    G
Sbjct: 197 LFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVG 256

Query: 517 MSV 519
            ++
Sbjct: 257 RAL 259


Lambda     K      H
   0.321    0.137    0.391 

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: 656
Number of extensions: 19
Number of successful extensions: 7
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: 521
Length of database: 515
Length adjustment: 35
Effective length of query: 486
Effective length of database: 480
Effective search space:   233280
Effective search space used:   233280
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: 52 (24.6 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