Alignments for a candidate for nupA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Paraburkholderia bryophila 376MFSha3.1

Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  333 bits (854), Expect = 9e-96
 Identities = 190/495 (38%), Positives = 292/495 (58%), Gaps = 8/495 (1%)

Query: 2   ANETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEG 61
           A   ++Q+  V+KRF   VA D ++L+L+ GE+HA+ GENGAGKSTLM I+SG     +G
Sbjct: 18  APREILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDG 77

Query: 62  EVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKK 121
            +  +GK     S S A   GI ++HQ   LV   +V ENI L  E  +G  +D +T   
Sbjct: 78  VICYEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNA 137

Query: 122 KILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITEL 181
                 +R GL+V P  L+  +S+ QQQ VEI K L   A +LI DEPT+ LT +E  +L
Sbjct: 138 NAQRCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQL 197

Query: 182 MQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGR 241
            +I++ L  +G +I+ I+H+LDE+  + DR+TV+R G+ I T +    T  E+   MVGR
Sbjct: 198 FRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGR 257

Query: 242 SVSFITEKAAAQP-KDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTE 300
           ++        + P + V++ ++DL   ++ G      LS D+R GEI+G AG+ G G+TE
Sbjct: 258 ALDDAYPPRESVPTEQVLMRVRDLQRTDTFGP-----LSFDLRKGEILGFAGLMGAGRTE 312

Query: 301 LVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIAL 360
           + +AI G  ++DSGSI+L +  +T + PR+     + ++ EDR +DGL L M VA NI L
Sbjct: 313 VARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITL 372

Query: 361 QTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDR 420
                  +S  GFL +++  + A   + E  +R       A +LSGGNQQK +I++ + R
Sbjct: 373 SNV--RAISSRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYR 430

Query: 421 NPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQ 480
              +L   +PTRG+DVGA   I+K + +   +G  V++IS EL E+L ++DRIAV H+G 
Sbjct: 431 GSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGL 490

Query: 481 IQGIVSPETTTKQEL 495
           I  ++    T+++E+
Sbjct: 491 ITAVLETRQTSQEEI 505



 Score = 93.2 bits (230), Expect = 2e-23
 Identities = 67/249 (26%), Positives = 123/249 (49%), Gaps = 9/249 (3%)

Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317
           +L++K ++ K   G + + G+ LD+R+GE+  V G +G G++ L+K I+G    D G I 
Sbjct: 22  ILQLKGVS-KRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVIC 80

Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYN 377
              K +            +  + ++ +   LV  ++VAENI L    K    +  F+DY 
Sbjct: 81  YEGKPVQFASTSDAQAAGIAIIHQELN---LVPHLSVAENIYLAREPK----RGPFVDYR 133

Query: 378 KINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVG 437
            +N++A+  ++   +          +LS   QQ   IA+ +  +  +LI+ +PT  L   
Sbjct: 134 TLNANAQRCLQRIGLN-VSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTES 192

Query: 438 AIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGI 497
               + + + + R +G A+L IS  LDE+  + DR+ V+ DG+        +TT  E+  
Sbjct: 193 ETVQLFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVA 252

Query: 498 LMVGGNINE 506
            MVG  +++
Sbjct: 253 RMVGRALDD 261



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 63/226 (27%), Positives = 106/226 (46%), Gaps = 10/226 (4%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           ++ +L+KGEI    G  GAG++ +   + G      G + +      I SP +A   GI 
Sbjct: 290 LSFDLRKGEILGFAGLMGAGRTEVARAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIA 349

Query: 85  MVHQHFM---LVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSERY--GLSVEPDA- 138
            + +      L  +  V  NI L N         L+ +++  +  +ERY   L++     
Sbjct: 350 YLSEDRKKDGLALSMPVAANITLSNVRAISSRGFLRFSEETAI--AERYVRELAIRTPTV 407

Query: 139 --LIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSII 196
             + R++S G QQ++ I K LYRG+ IL FDEPT  +       + ++M  L  +G  ++
Sbjct: 408 KQIARNLSGGNQQKIVISKWLYRGSRILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVV 467

Query: 197 LITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRS 242
           LI+ +L E+  + DRI V   G     +E    + +E+     GRS
Sbjct: 468 LISSELPELLGMTDRIAVFHEGLITAVLETRQTSQEEILHYASGRS 513


Lambda     K      H
   0.315    0.135    0.365 

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: 619
Number of extensions: 39
Number of successful extensions: 7
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: 506
Length of database: 515
Length adjustment: 35
Effective length of query: 471
Effective length of database: 480
Effective search space:   226080
Effective search space used:   226080
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: 42 (22.0 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