Alignments for a candidate for HSERO_RS05250 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Herbaspirillum seropedicae SmR1

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS22465 HSERO_RS22465 sugar ABC transporter

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__HerbieS:HSERO_RS22465
          Length = 518

 Score =  392 bits (1006), Expect = e-113
 Identities = 225/503 (44%), Positives = 324/503 (64%), Gaps = 17/503 (3%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS--GDI 79
           ++ ++ + K F GV AL+    ++  GE   L GENGAGKSTLMKILSGVY   +  G+I
Sbjct: 5   LLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWEGEI 64

Query: 80  LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139
           L DGKP++    R  +A GI IIHQEL L+  LS A+NIF+G E     G  ++   + R
Sbjct: 65  LWDGKPLQAHSVRDTEAAGIVIIHQELMLVPELSVAENIFMGHEITLPGGR-MNYPAMYR 123

Query: 140 QAAAIFARMRL-DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198
           +A  +   + + D++ + PV +     QQ+VEIAKAL+ D+R+LI+DEP+++L  +EI  
Sbjct: 124 RAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSSLTASEIGV 183

Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           L +II+DL+A+GV  VYISHK+DE+ ++ D +SV+RDGK+IAT PMQE  +D II+ MVG
Sbjct: 184 LLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVDKIITQMVG 243

Query: 259 RALDGEQRIPPDTSR--NDVVLEVRGLN-------RGRAIRDVSFTLRKGEILGFAGLMG 309
           R +     + P+ +    +VVLE R +        R + + DVSF++R+GEILG AGL+G
Sbjct: 244 REITA---MYPERNHAIGEVVLEARNITCYDIDNPRRKRVDDVSFSVRRGEILGIAGLVG 300

Query: 310 AGRTEVARAIFGA-DPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDV 368
           AGRTE+  AIFGA      G++++ G  A   SP  ++  G+  + EDRKH G+   +DV
Sbjct: 301 AGRTELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIRRGLCMVPEDRKHHGIVPDLDV 360

Query: 369 QANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428
             NI L+ + RF+R   +D  A  +  Q  + ++ +KT +       LSGGNQQK V+AK
Sbjct: 361 GQNITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRVKTATPFLPITSLSGGNQQKAVLAK 420

Query: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488
            LL    +L  DEPTRG+DVGAK+EIY+L+  LA+ G AI+M+SSEL EVL +S RVLV+
Sbjct: 421 MLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLAIIMVSSELAEVLGVSDRVLVI 480

Query: 489 CEGRITGELARADATQEKIMQLA 511
            EGR+ G+    + +QE ++  A
Sbjct: 481 GEGRLRGDFVNDNLSQETVLAAA 503



 Score = 98.6 bits (244), Expect = 5e-25
 Identities = 66/241 (27%), Positives = 121/241 (50%), Gaps = 11/241 (4%)

Query: 38  LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQ-RDSGDILLDGKPVEITEPRQAQA 96
           +D+  F +  GE+  + G  GAG++ L+  + G Y+ R  G +LL+GKP + + P ++  
Sbjct: 280 VDDVSFSVRRGEILGIAGLVGAGRTELVSAIFGAYRGRYEGQVLLEGKPADTSSPLKSIR 339

Query: 97  LGIGIIHQELN---LMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM- 152
            G+ ++ ++     ++  L   QNI +    R + G  ID     +       RMR+   
Sbjct: 340 RGLCMVPEDRKHHGIVPDLDVGQNITLTVLNRFSRGSRIDGSAELKTIQDEIGRMRVKTA 399

Query: 153 DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVG 212
            P  P+  L+   QQ   +AK L    +VLI+DEPT  ++    AE++R+I +L   G+ 
Sbjct: 400 TPFLPITSLSGGNQQKAVLAKMLLAQPKVLILDEPTRGVDVGAKAEIYRLISELAKAGLA 459

Query: 213 IVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQRIPPDTS 272
           I+ +S ++ E+  ++DRV V+ +G+          S +T+++  +       Q +P  T 
Sbjct: 460 IIMVSSELAEVLGVSDRVLVIGEGRLRGDFVNDNLSQETVLAAAI------NQPVPQATP 513

Query: 273 R 273
           R
Sbjct: 514 R 514



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 66/250 (26%), Positives = 114/250 (45%), Gaps = 14/250 (5%)

Query: 274 NDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEA-- 327
           ++ +LE++G+ +     RA+  +   +R GE +G  G  GAG++ + + + G  P     
Sbjct: 2   SEYLLEMKGIVKSFGGVRALNGIDIKIRPGECVGLCGENGAGKSTLMKILSGVYPHGTWE 61

Query: 328 GEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRV--GF 385
           GEI+  G      S  D  A GI  + ++     L   + V  NI    MG    +  G 
Sbjct: 62  GEILWDGKPLQAHSVRDTEAAGIVIIHQELM---LVPELSVAENIF---MGHEITLPGGR 115

Query: 386 MDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRG 445
           M+  A+   A+  +R+L +   +V        GG+QQ + IAK L +D  +L  DEP+  
Sbjct: 116 MNYPAMYRRAEELMRELNMPDINVALPVSQYGGGHQQLVEIAKALNKDARLLILDEPSSS 175

Query: 446 IDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQE 505
           +       + K++  L  +G A V IS +L EV  +   + V+ +G+        +   +
Sbjct: 176 LTASEIGVLLKIIKDLKARGVACVYISHKLDEVAEVCDTISVIRDGKHIATTPMQEMDVD 235

Query: 506 KIMQLATQRE 515
           KI+     RE
Sbjct: 236 KIITQMVGRE 245


Lambda     K      H
   0.320    0.135    0.372 

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: 689
Number of extensions: 31
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 520
Length of database: 518
Length adjustment: 35
Effective length of query: 485
Effective length of database: 483
Effective search space:   234255
Effective search space used:   234255
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources