Alignments for a candidate for araVsh in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Herbaspirillum seropedicae SmR1

Align ABC transporter related (characterized, see rationale)
to candidate HSERO_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__HerbieS:HSERO_RS05175
          Length = 516

 Score =  466 bits (1200), Expect = e-136
 Identities = 252/501 (50%), Positives = 340/501 (67%), Gaps = 7/501 (1%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LEL  I K + GVKAL DV LRLF GEVH L+G+NGAGKSTL+KV+TG    D G I  
Sbjct: 12  MLELSGIHKAFAGVKALTDVGLRLFPGEVHTLMGQNGAGKSTLIKVLTGVHEPDGGKIEL 71

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G      + ++AQ  GISTVYQEVNL PNL+VA+N+F+G  P R G I +K ++  +R 
Sbjct: 72  DGRAIAPASTLEAQALGISTVYQEVNLCPNLSVAENIFVGRYPTRFGRIDWKSVHTQSRQ 131

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +L Q ++DIDV+APLS Y +A+QQ++AI+R +++SAKVL+LDEPT+SLD  EVQ LF +L
Sbjct: 132 LLQQLQIDIDVAAPLSSYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQQLFKVL 191

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLG-RSLQ 242
            +L+ +G+AI+F+THFLDQ Y+ISDRITVLRNG   GEYL +EL +  L+  M+G  ++ 
Sbjct: 192 RRLREQGMAILFVTHFLDQTYEISDRITVLRNGVREGEYLVSELSRLDLVNKMVGVTAVD 251

Query: 243 EQLVD------KQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSG 296
            + V+        E       A AV L  E    +G +   +L + +G+  GL GLLGSG
Sbjct: 252 HRKVEAGAEALASELSTDAAAAGAVFLQAEGFGRRGVLAPQDLQLRRGEVFGLCGLLGSG 311

Query: 297 RSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIREN 356
           R+E+   +FG D  D G + + G+++ L+ P DAI+AGI  C EDRK +G I  LS+REN
Sbjct: 312 RTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGFCSEDRKKEGAILELSVREN 371

Query: 357 IILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLA 416
           IILALQAR G +R L   RQ +IA  ++  L I T D + PI  LSGGNQQK +LARWLA
Sbjct: 372 IILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETPIGLLSGGNQQKALLARWLA 431

Query: 417 IEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDR 476
            +P +L+LDEPTRGID+ A  EI+  +  +C +GMS+L  SSE+ E++  S++++VLRDR
Sbjct: 432 TDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFISSEIPEVLRCSDRMLVLRDR 491

Query: 477 YAVRELSGAELTSQHVMQAIA 497
            A  E    EL  Q V+Q IA
Sbjct: 492 RACGEYRRGELDEQSVLQVIA 512



 Score = 96.7 bits (239), Expect = 2e-24
 Identities = 68/232 (29%), Positives = 115/232 (49%), Gaps = 10/232 (4%)

Query: 16  GVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMD 75
           GV A +D+ LR   GEV  L G  G+G++ + +++ GA   D G +   G+    N P D
Sbjct: 287 GVLAPQDLQLR--RGEVFGLCGLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRD 344

Query: 76  AQKAGI---STVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQFKL-- 130
           A  AGI   S   ++   +  L+V +N+ L  + R+ GL          +      K   
Sbjct: 345 AIAAGIGFCSEDRKKEGAILELSVRENIILALQARQ-GLFRVLPRKRQNQIAADYVKWLG 403

Query: 131 --DIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKA 188
               D+  P+   S   QQ   +AR +A    +L+LDEPT  +D +  Q +   +  +  
Sbjct: 404 IKTADLETPIGLLSGGNQQKALLARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCR 463

Query: 189 KGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS 240
           KG++I+FI+  + +V + SDR+ VLR+ +  GEY   EL +  +++ + G +
Sbjct: 464 KGMSILFISSEIPEVLRCSDRMLVLRDRRACGEYRRGELDEQSVLQVIAGET 515


Lambda     K      H
   0.319    0.136    0.377 

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: 638
Number of extensions: 21
Number of successful extensions: 6
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: 499
Length of database: 516
Length adjustment: 34
Effective length of query: 465
Effective length of database: 482
Effective search space:   224130
Effective search space used:   224130
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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