Alignments for a candidate for HSERO_RS03640 in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Azospirillum brasilense Sp245

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__azobra:AZOBR_RS06625
          Length = 511

 Score =  288 bits (736), Expect = 4e-82
 Identities = 179/492 (36%), Positives = 272/492 (55%), Gaps = 18/492 (3%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P L+ RG+ K FGA  A  D+ L +  G IH ++GENGAGKST+M ++ G    D G IL
Sbjct: 6   PALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTIL 65

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           +DGRPVA+R P  + AAGI +++Q   +    +V  NV +G+E     G +  AA  +R 
Sbjct: 66  VDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAE-----GGVTLAAGMARA 120

Query: 125 DAVLRQLGAGFGAS-DL---AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180
              L +L   +G   DL    G L +  QQ+VEI +AL   + I+I+DEPT  L+ +ET+
Sbjct: 121 RTELTRLARDYGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETD 180

Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240
            LF ++R LR++G  ++ I+H++ E+  L D VTV+R G  V  +       E + ++MV
Sbjct: 181 HLFRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMV 240

Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRT 299
           GR +    +     P  A    + + VR  AG  +++     VRAGE++G AG+ G G++
Sbjct: 241 GRKVLLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQS 300

Query: 300 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA----GIAYVPEDRKGQGL---FLQM 352
           EL   L G  P + G + L G  +     R   R     G+ +VPEDR+  GL   F   
Sbjct: 301 ELLEALAGMRPPAEGSVRLRGEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFEAQ 360

Query: 353 AVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLL 412
             A        + + RL L+  R+L     + +   +V+   P  P    SGGNQQK++L
Sbjct: 361 ECAILGHQGDPAFNGRL-LMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVL 419

Query: 413 ARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVL 472
           AR +E  P +L++ +PTRGVDI A   I++ +  L  QG A++++S EL E+  + DR+L
Sbjct: 420 AREMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRIL 479

Query: 473 VMREGMITGELA 484
           VM +G + GE+A
Sbjct: 480 VMFDGRLVGEVA 491



 Score = 99.8 bits (247), Expect = 2e-25
 Identities = 73/242 (30%), Positives = 118/242 (48%), Gaps = 10/242 (4%)

Query: 276 RPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAG 335
           R  S  V  G + G  G  GAG++ +  +++G  P  GG IL++GRPV +  PR A+ AG
Sbjct: 24  RDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTILVDGRPVAVRSPRDALAAG 83

Query: 336 IAYVPEDRKGQGLFLQMAVAANATMNVASRHT-RLGLVRSRS-LGGVARAAIQRLNVKVA 393
           I  V +      L     V  N  +      T   G+ R+R+ L  +AR     +++   
Sbjct: 84  IGMVHQHFM---LVDPFTVLENVLLGAEGGVTLAAGMARARTELTRLARDYGLEVDL--- 137

Query: 394 HPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVA 453
             + PVG+L  G QQ+V + + L     +LILDEPT  +       +++++  L  QG  
Sbjct: 138 --DRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDHLFRILRALREQGKT 195

Query: 454 VVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSSP 513
           VV+I+ +L E++ + D V VMR G +   +A A  ++E +  L     V        ++P
Sbjct: 196 VVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGRKVLLRVEKVPATP 255

Query: 514 TP 515
            P
Sbjct: 256 GP 257



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 72/256 (28%), Positives = 121/256 (47%), Gaps = 28/256 (10%)

Query: 6   LLQMRGIRKSFGATLA-LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           +L++ G+    GA +  +  + LT+R GEI  + G +G G+S L++ L+G+  P +G + 
Sbjct: 259 VLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQSELLEALAGMRPPAEGSVR 318

Query: 65  LDGRPVALRDPGAS----RAAGINLI--------------YQELAVAPNISVAANVFMGS 106
           L G  +       +    RA G+  +               QE A+  +    A  F G 
Sbjct: 319 LRGEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFEAQECAILGHQGDPA--FNGR 376

Query: 107 ELRTRLGLIDHAAMRSRTDAV-LRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIV 165
            L  R  L D  A  S  DA  +R       A++ +G      QQ++ +AR +     ++
Sbjct: 377 LLMDRRALFDRCA--SEMDAYDVRPRDPRLPAANFSG----GNQQKIVLAREMERNPDLL 430

Query: 166 IMDEPTAALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGEL 225
           ++ +PT  +     E +   +  LRD+G AI+ +S  + E+ AL+DR+ V+ DG  VGE+
Sbjct: 431 LVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRILVMFDGRLVGEV 490

Query: 226 VRDEIDSERIVQMMVG 241
              E D  R+  MM G
Sbjct: 491 APGEADERRLGLMMAG 506


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: 762
Number of extensions: 52
Number of successful extensions: 9
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: 521
Length of database: 511
Length adjustment: 35
Effective length of query: 486
Effective length of database: 476
Effective search space:   231336
Effective search space used:   231336
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