GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11890 in Sinorhizobium meliloti 1021

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein

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



>FitnessBrowser__Smeli:SMc02325
          Length = 503

 Score =  430 bits (1105), Expect = e-125
 Identities = 216/488 (44%), Positives = 327/488 (67%)

Query: 33  VSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVT 92
           +SK FPGV ALSDV L + PGSV AL+GENGAGKSTL+KI+ GIYQPDAG +RL     T
Sbjct: 10  ISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIRLGDTETT 69

Query: 93  FDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTAQLLERL 152
           F T LAA +AG+  IHQE  L   +S+AENI++G    N F +ID ++++     LL R 
Sbjct: 70  FPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNADAQALLGRA 129

Query: 153 RINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKA 212
             + DP  ++ +L IA++ +V IA+A+S D+ ++IMDEPT+A++ KE+  L+ +I  LKA
Sbjct: 130 GADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELYDLIERLKA 189

Query: 213 QGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELSQLFPVR 272
            GK +++I+HK +E+F IAD   VFRDGA IG      +  D L+ MMVGR +  ++P +
Sbjct: 190 DGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGRAVGSVYPKK 249

Query: 273 EKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGE 332
           E  IG  +++V   R    F+ ++F+L  GEILG  GL+G+GR+   +++ GIT    G 
Sbjct: 250 EVTIGQPVLTVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFMQSLIGITRPSAGA 309

Query: 333 ICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQK 392
           + LDG+ + I  P  AI  G   + E+R   G    + + +N+ +  L H + +GF++  
Sbjct: 310 VKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPSLSHTSRSGFLRLA 369

Query: 393 ALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVG 452
              AL  +   +L ++  +L+Q + TLSGGNQQK ++A+WL T P+++ILDEPT+GID+G
Sbjct: 370 EEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKVIILDEPTKGIDIG 429

Query: 453 AKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQ 512
           +KA ++  +S LA++G++VIM+SSE+PE++GMSDRV+VM EG + G  +RSE T E++++
Sbjct: 430 SKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYERSELTAEKLVR 489

Query: 513 LASGMSVR 520
            A+G+  +
Sbjct: 490 AAAGIETQ 497


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: 622
Number of extensions: 28
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 521
Length of database: 503
Length adjustment: 35
Effective length of query: 486
Effective length of database: 468
Effective search space:   227448
Effective search space used:   227448
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