GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Sinorhizobium meliloti 1021

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate SMc02337 SMc02337 ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__Smeli:SMc02337
          Length = 501

 Score =  395 bits (1014), Expect = e-114
 Identities = 216/499 (43%), Positives = 314/499 (62%), Gaps = 7/499 (1%)

Query: 1   MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60
           M+  +    I K F GV+AL GV FD+  G+VH L+GENGAGKSTL+++L GE +P SG 
Sbjct: 1   MTVLVSLSGISKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGT 60

Query: 61  VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF 120
           V I G  ++ +    +   GI+VIHQEL   PDLTVAEN+ LG+LP     VN R  ++ 
Sbjct: 61  VSIHGETMQHSGPRGAAGRGISVIHQELALAPDLTVAENIFLGRLPRI---VNHRRLRKA 117

Query: 121 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 180
             E LE +G  +DP     +L++A +Q+VEI KAL   AR+I  DEPT+ L++ + E L 
Sbjct: 118 ASEILERLGFDIDPAIHAGRLTVAHQQVVEIAKALSNRARIIVFDEPTAVLANTDAERLL 177

Query: 181 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR 240
            ++R+LRA     +YISHR++E+++L D  T+ +DG  + +  T      D +++ MVGR
Sbjct: 178 AIIRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLET-SATDVDAVIARMVGR 236

Query: 241 EISDIY-NYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLV 299
           ++S ++ + + R  GEV    + +      +  SF VR GE+VG  GLVG+GR+E+  LV
Sbjct: 237 QMSALFPSKAGRVPGEVVVRVRNVSRGRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLV 296

Query: 300 YGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH 359
           +GAD    G + L+GKP+ + S  EA+R  I L PEDRK++G++  A +  N  ++  R 
Sbjct: 297 FGADKMDSGTVELNGKPLHLSSPREAVRARIGLVPEDRKQQGVILDAPIRINTTLAKIRS 356

Query: 360 YLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVV 419
             R+G FLD  KE + A      +++K  S    +  LSGGNQQK  L++W    D  ++
Sbjct: 357 ISRLG-FLDAGKERQVAVALGAEMRLKASSVDAPVSSLSGGNQQKVALAKWF-HADCDLL 414

Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479
           ILDEPTRG+DVGAK EIYN+I  LA+ G AI++ISSE  E+ G+ DR++VM +G I GEL
Sbjct: 415 ILDEPTRGVDVGAKGEIYNLINDLAKAGKAILVISSEHQELFGICDRVLVMAEGAIVGEL 474

Query: 480 TRKDATEQSVLSLALPQSS 498
           T    TEQ +L+LA+ +S+
Sbjct: 475 TESKFTEQQLLTLAMTRSA 493



 Score = 60.8 bits (146), Expect = 1e-13
 Identities = 57/242 (23%), Positives = 105/242 (43%), Gaps = 11/242 (4%)

Query: 260 AKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKV 319
           +K   G    +   F++R GE+    G  GAG+S LM ++ G      G + + G+ ++ 
Sbjct: 11  SKNFSGVQALKGVDFDLRAGEVHALVGENGAGKSTLMRVLAGEMKPTSGTVSIHGETMQH 70

Query: 320 RSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAETADRF 379
                A   GI +     +E  +    TV+ENI +       R+   ++ ++  + A   
Sbjct: 71  SGPRGAAGRGISVI---HQELALAPDLTVAENIFLG------RLPRIVNHRRLRKAASEI 121

Query: 380 IKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYNV 439
           ++ L           R L+  +QQ   +++ L+    ++++ DEPT  +       +  +
Sbjct: 122 LERLGFDIDPAIHAGR-LTVAHQQVVEIAKALSNR-ARIIVFDEPTAVLANTDAERLLAI 179

Query: 440 IYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSLALPQSST 499
           I +L   G   V IS  L EV  +SDRI VM+ G     L        +V++  + +  +
Sbjct: 180 IRELRAGGTGAVYISHRLNEVFDLSDRITVMKDGSHVETLETSATDVDAVIARMVGRQMS 239

Query: 500 AL 501
           AL
Sbjct: 240 AL 241


Lambda     K      H
   0.320    0.136    0.385 

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: 628
Number of extensions: 31
Number of successful extensions: 9
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: 512
Length of database: 501
Length adjustment: 34
Effective length of query: 478
Effective length of database: 467
Effective search space:   223226
Effective search space used:   223226
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