Alignments for a candidate for fruK in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Herbaspirillum seropedicae SmR1

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate HSERO_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__HerbieS:HSERO_RS05175
          Length = 516

 Score =  454 bits (1167), Expect = e-132
 Identities = 238/508 (46%), Positives = 344/508 (67%), Gaps = 8/508 (1%)

Query: 2   TDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA 61
           T   P++ + GI   F GVKAL  V L L+PGEVH LMG+NGAGKST+IK LTGV++ + 
Sbjct: 7   TQARPMLELSGIHKAFAGVKALTDVGLRLFPGEVHTLMGQNGAGKSTLIKVLTGVHEPDG 66

Query: 62  GSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTH 121
           G I +DG+      TL+AQ  GI+TVYQEVNLC NLSV EN+ +G        IDWK  H
Sbjct: 67  GKIELDGRAIAPASTLEAQALGISTVYQEVNLCPNLSVAENIFVGRYPTRFGRIDWKSVH 126

Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181
             +++ L Q+ ++ ID   PLSS  +A+QQ+VAI+RA+ ++AKVLILDEPTSSLD  EV+
Sbjct: 127 TQSRQLLQQLQID-IDVAAPLSSYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQ 185

Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241
            LF ++R++R+ G+AILFV+HFLDQ YEI+DR+T+LRNG    E +  +  R +L+  M+
Sbjct: 186 QLFKVLRRLREQGMAILFVTHFLDQTYEISDRITVLRNGVREGEYLVSELSRLDLVNKMV 245

Query: 242 GKSAAELSQI--GAKKARREITPGEKP----IVDVKGLGKKGTINPVDVDIYKGEVVGFA 295
           G +A +  ++  GA+    E++          +  +G G++G + P D+ + +GEV G  
Sbjct: 246 GVTAVDHRKVEAGAEALASELSTDAAAAGAVFLQAEGFGRRGVLAPQDLQLRRGEVFGLC 305

Query: 296 GLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGD 355
           GLLGSGRTE+ RLL+GAD+ D G   + GK+V ++ P  A+   I + +E+R+ EG I +
Sbjct: 306 GLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGFCSEDRKKEGAILE 365

Query: 356 LTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVL 415
           L+VR+NI++ALQA +G+F+ +P+K  + I   Y+K L ++ AD + P+  LSGGNQQK L
Sbjct: 366 LSVRENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETPIGLLSGGNQQKAL 425

Query: 416 IGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDI 475
           + RWLAT P +LILDEPTRGID+ AK EI   V+ +  +GM ++FISSE+ EV+R SD +
Sbjct: 426 LARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFISSEIPEVLRCSDRM 485

Query: 476 EVLKDRHKIAEIENDDTVSQATIVETIA 503
            VL+DR    E    + + + ++++ IA
Sbjct: 486 LVLRDRRACGEYRRGE-LDEQSVLQVIA 512



 Score = 97.4 bits (241), Expect = 1e-24
 Identities = 63/224 (28%), Positives = 117/224 (52%), Gaps = 5/224 (2%)

Query: 27  DLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIAT 86
           DL L  GEV  L G  G+G++ M + L G  + + G + ++GK  + N   DA  AGI  
Sbjct: 293 DLQLRRGEVFGLCGLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGF 352

Query: 87  VYQE---VNLCTNLSVGENVMLGHEKR-GPFGI-DWKKTHEAAKKYLAQMGLESIDPHTP 141
             ++         LSV EN++L  + R G F +   K+ ++ A  Y+  +G+++ D  TP
Sbjct: 353 CSEDRKKEGAILELSVRENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETP 412

Query: 142 LSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFVS 201
           +  +S   QQ   +AR +  +  +LILDEPT  +D    +++   +  +   G++ILF+S
Sbjct: 413 IGLLSGGNQQKALLARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFIS 472

Query: 202 HFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
             + ++   +DR+ +LR+ +   E    +     ++ ++ G++A
Sbjct: 473 SEIPEVLRCSDRMLVLRDRRACGEYRRGELDEQSVLQVIAGETA 516


Lambda     K      H
   0.316    0.135    0.376 

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: 624
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: 513
Length of database: 516
Length adjustment: 35
Effective length of query: 478
Effective length of database: 481
Effective search space:   229918
Effective search space used:   229918
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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