Aligments for a candidate for HSERO_RS03640 in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for HSERO_RS03640 in Herbaspirillum seropedicae SmR1

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05175 HSERO_RS05175 sugar ABC
           transporter ATP-binding protein
          Length = 516

 Score =  383 bits (983), Expect = e-110
 Identities = 205/501 (40%), Positives = 318/501 (63%), Gaps = 10/501 (1%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P+L++ GI K+F    AL+D+ L + PGE+H LMG+NGAGKSTL+KVL+GVH PD G+I 
Sbjct: 11  PMLELSGIHKAFAGVKALTDVGLRLFPGEVHTLMGQNGAGKSTLIKVLTGVHEPDGGKIE 70

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           LDGR +A      ++A GI+ +YQE+ + PN+SVA N+F+G    TR G ID  ++ +++
Sbjct: 71  LDGRAIAPASTLEAQALGISTVYQEVNLCPNLSVAENIFVG-RYPTRFGRIDWKSVHTQS 129

Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184
             +L+QL      +       +A QQ V I+RAL   ++++I+DEPT++L E E +QLF 
Sbjct: 130 RQLLQQLQIDIDVAAPLSSYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQQLFK 189

Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244
           V+RRLR++G+AI++++H + + Y ++DR+TVLR+G   GE +  E+    +V  MVG + 
Sbjct: 190 VLRRLREQGMAILFVTHFLDQTYEISDRITVLRNGVREGEYLVSELSRLDLVNKMVGVTA 249

Query: 245 SEFYQHQRIAPADAAQLPT--------VMQVRALAG-GKIRPASFDVRAGEVLGFAGLVG 295
            +  + +  A A A++L T         +Q       G + P    +R GEV G  GL+G
Sbjct: 250 VDHRKVEAGAEALASELSTDAAAAGAVFLQAEGFGRRGVLAPQDLQLRRGEVFGLCGLLG 309

Query: 296 AGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVA 355
           +GRTE+ARLLFGAD    G + +EG+ V ++ PR A+ AGI +  EDRK +G  L+++V 
Sbjct: 310 SGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGFCSEDRKKEGAILELSVR 369

Query: 356 ANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARW 415
            N  + + +R     ++  +    +A   ++ L +K A  ETP+G LSGGNQQK LLARW
Sbjct: 370 ENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETPIGLLSGGNQQKALLARW 429

Query: 416 LEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMR 475
           L   P +LILDEPTRG+D+ AK EI   V  +  +G++++ ISSE+PEV+   DR+LV+R
Sbjct: 430 LATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFISSEIPEVLRCSDRMLVLR 489

Query: 476 EGMITGELAGAAITQENIMRL 496
           +    GE     + +++++++
Sbjct: 490 DRRACGEYRRGELDEQSVLQV 510



 Score = 98.2 bits (243), Expect = 6e-25
 Identities = 69/238 (28%), Positives = 120/238 (50%), Gaps = 11/238 (4%)

Query: 14  KSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALR 73
           + FG    L+   L +R GE+  L G  G+G++ + ++L G    D G++ ++G+ V L 
Sbjct: 281 EGFGRRGVLAPQDLQLRRGEVFGLCGLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLN 340

Query: 74  DPGASRAAGINLIYQEL---AVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQ 130
            P  + AAGI    ++         +SV  N+ +   L+ R GL      R R + +   
Sbjct: 341 VPRDAIAAGIGFCSEDRKKEGAILELSVRENIILA--LQARQGLF-RVLPRKRQNQIAAD 397

Query: 131 L--GAGFGASDLA---GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
                G   +DL    G LS   QQ+  +AR L     ++I+DEPT  +  R  +++ + 
Sbjct: 398 YVKWLGIKTADLETPIGLLSGGNQQKALLARWLATDPGMLILDEPTRGIDVRAKQEIMDF 457

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
           V  +  +G++I++IS  + EV   +DR+ VLRD    GE  R E+D + ++Q++ G +
Sbjct: 458 VIAMCRKGMSILFISSEIPEVLRCSDRMLVLRDRRACGEYRRGELDEQSVLQVIAGET 515


Lambda     K      H
   0.320    0.135    0.378 

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: 675
Number of extensions: 29
Number of successful extensions: 7
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: 521
Length of database: 516
Length adjustment: 35
Effective length of query: 486
Effective length of database: 481
Effective search space:   233766
Effective search space used:   233766
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 preprint 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

GapMind for catabolism of small carbon sources