Alignments for a candidate for iatA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Herbaspirillum seropedicae SmR1

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__HerbieS:HSERO_RS03640
          Length = 502

 Score =  404 bits (1038), Expect = e-117
 Identities = 227/495 (45%), Positives = 319/495 (64%), Gaps = 8/495 (1%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           LL +  + KSF    AL  + L +  GE+HAL+GENGAGKSTL+K+LS  HA D G +  
Sbjct: 10  LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 69

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADA 121
            G+ +  RD P   +  GI  IYQE  + P +SVA N+++G E R RLGL+D + +R+  
Sbjct: 70  DGRPVALRD-PGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 128

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
            A+L  LG           L++AEQQ VEIA+A+   +R++IMDEPTAALS RE ++L  
Sbjct: 129 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 188

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
           ++  L+   +++IY+SHR+ EV A+ DR TV+RDG FV      +++   +V++MVGR +
Sbjct: 189 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 248

Query: 242 -EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300
            EF + +R  P  A  L     T    R  A G +R  SF  R GE++G AGLVGAGRT+
Sbjct: 249 SEFYQHQRIAPADAAQLP----TVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 304

Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360
           LARL+FGADP + G +L++ +P+ +  PR A++AGI  VPEDRK QG FL  ++  N ++
Sbjct: 305 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 364

Query: 361 PSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420
                 + LG  V  R+   +     Q+L +K+A  ET +GKLSGGNQQKVLL R + + 
Sbjct: 365 NVASRHTRLGL-VRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 423

Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480
           PKVLI+DEPTRG+DI AK+E++Q++  LA  GVAVVVISSEL EV+ + DR++V REG+I
Sbjct: 424 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 483

Query: 481 VADLDAQTATEEGLM 495
             +L     T+E +M
Sbjct: 484 TGELAGAAITQENIM 498



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 66/231 (28%), Positives = 109/231 (47%), Gaps = 20/231 (8%)

Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334
           L  +    R GEI  L G  GAG++ L +++ G      G +L+D +P+ LR P  +  A
Sbjct: 26  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAA 85

Query: 335 GIMLV-------PEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQ 387
           GI L+       P        F+   +R  L L            +D  A R   +   +
Sbjct: 86  GINLIYQELAVAPNISVAANVFMGSELRTRLGL------------IDHAAMRSRTDAVLR 133

Query: 388 KLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSD 447
           +L      ++ A G+LS   QQ+V + RA+    +++I+DEPT  +      ++  V+  
Sbjct: 134 QLGAGFGASDLA-GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRR 192

Query: 448 LADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYM 498
           L D G+A++ IS  +AEV A++DR+ V R+G  V +L       E ++  M
Sbjct: 193 LRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMM 243



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 63/216 (29%), Positives = 109/216 (50%), Gaps = 7/216 (3%)

Query: 26  VGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIY 85
           V  GEV    G  GAG++ L ++L  A     G +   G+ +   D P    + GIA + 
Sbjct: 286 VRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHI-DQPRAAMRAGIAYVP 344

Query: 86  QEFN---LFPELSVAEN--MYLGREPRRLGLVDWSRLRADAQALLNDLGLPL-NPDAPVR 139
           ++     LF +++VA N  M +     RLGLV    L   A+A +  L + + +P+ PV 
Sbjct: 345 EDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVG 404

Query: 140 GLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHR 199
            L+   QQ V +A+ + +  +++I+DEPT  +       ++ ++  L ++ V+V+ +S  
Sbjct: 405 KLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSE 464

Query: 200 LGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRL 235
           L EV  +CDR  VMR+G        A +   +++RL
Sbjct: 465 LPEVIGICDRVLVMREGMITGELAGAAITQENIMRL 500


Lambda     K      H
   0.320    0.136    0.380 

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: 699
Number of extensions: 38
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: 515
Length of database: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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