GapMind for catabolism of small carbon sources

 

Aligments 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)



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