GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iatA in Sinorhizobium meliloti 1021

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>lcl|FitnessBrowser__Smeli:SMc02337 SMc02337 ABC transporter
           ATP-binding protein
          Length = 501

 Score =  392 bits (1006), Expect = e-113
 Identities = 225/506 (44%), Positives = 322/506 (63%), Gaps = 19/506 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           L+ +S +SK+F GV+AL  VD  +  GEVHAL+GENGAGKSTL+++L+      +GTV+ 
Sbjct: 4   LVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTVSI 63

Query: 63  AGQVLD---PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119
            G+ +    PR A  R    GI+ I+QE  L P+L+VAEN++LGR PR   +V+  RLR 
Sbjct: 64  HGETMQHSGPRGAAGR----GISVIHQELALAPDLTVAENIFLGRLPR---IVNHRRLRK 116

Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179
            A  +L  LG  ++P      LTVA QQ+VEIAKA++  AR+I+ DEPTA L+  + +RL
Sbjct: 117 AASEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERL 176

Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
            AII  L+A     +Y+SHRL EV  + DR TVM+DG  V + + +  +V  ++  MVGR
Sbjct: 177 LAIIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGR 236

Query: 240 HVE-FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298
            +      K  R PG VV++V  V+           +R VSF+ R GE+VGL GLVG+GR
Sbjct: 237 QMSALFPSKAGRVPGEVVVRVRNVSRGRK-------VRDVSFSVRAGEVVGLGGLVGSGR 289

Query: 299 TDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358
           T++ARL+FGAD + +G V ++ KPL L SPR+A++A I LVPEDRKQQG  LD  IR N 
Sbjct: 290 TEVARLVFGADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINT 349

Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418
           +L  ++++S LG ++D   ER +      ++R+K +  +  +  LSGGNQQKV L +   
Sbjct: 350 TLAKIRSISRLG-FLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWFH 408

Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREG 478
               +LI+DEPTRG+D+GAK E++ +++DLA  G A++VISSE  E+  + DR++V  EG
Sbjct: 409 ADCDLLILDEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEG 468

Query: 479 VIVADLDAQTATEEGLMAYMATGTDR 504
            IV +L     TE+ L+    T + R
Sbjct: 469 AIVGELTESKFTEQQLLTLAMTRSAR 494


Lambda     K      H
   0.320    0.136    0.380 

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: 703
Number of extensions: 36
Number of successful extensions: 9
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: 515
Length of database: 501
Length adjustment: 34
Effective length of query: 481
Effective length of database: 467
Effective search space:   224627
Effective search space used:   224627
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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