Aligments for a candidate for HSERO_RS00870 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Aligments for a candidate for HSERO_RS00870 in Acidovorax sp. GW101-3H11

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Ac3H11_552 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_552
          Length = 384

 Score =  513 bits (1322), Expect = e-150
 Identities = 247/371 (66%), Positives = 294/371 (79%), Gaps = 1/371 (0%)

Query: 6   KLTVVAAIAAAAGVASAQE-QVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTI 64
           +++ + A+A AA VASAQ+ Q VKI H  PVSG  AH GKD ENG R+AI++LNAQ + I
Sbjct: 13  RISALTAVALAASVASAQDVQTVKIAHAGPVSGGIAHIGKDTENGVRLAIDDLNAQNLVI 72

Query: 65  GGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124
           GGKKIKFE+ AEDDA DP+Q TA AQKLCD KVAGVVGHL SGT+IPAS +Y  C +PH+
Sbjct: 73  GGKKIKFEIAAEDDAGDPRQATAVAQKLCDQKVAGVVGHLQSGTSIPASAIYAKCDLPHI 132

Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184
           T +A+NP+LTKPG+KTTFR+IANDNALGA LA +  D  KLK+VAIIDDRTAYGQGVA V
Sbjct: 133 TASASNPDLTKPGHKTTFRLIANDNALGAALALFGADHQKLKSVAIIDDRTAYGQGVASV 192

Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244
           FK TA  KG+KVV E+FT DKATDFMAILTAIK K PDAIFYGG+D Q GPMLRQMEQLG
Sbjct: 193 FKATAQQKGLKVVAEEFTNDKATDFMAILTAIKNKKPDAIFYGGLDAQAGPMLRQMEQLG 252

Query: 245 MGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQF 304
           +GNVKYFGGD +CT ++ +L+     L NV CA GG+S+ KM GG  WK +YDAK+P QF
Sbjct: 253 LGNVKYFGGDALCTEKLPELSGKTPALKNVTCATGGASVDKMQGGADWKKRYDAKFPGQF 312

Query: 305 QVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITL 364
           Q+YSPY YDA  ++ DAMKRANSVDPKV+ P LAK+ +KGVT+ IAF   GE+  PA+TL
Sbjct: 313 QIYSPYAYDAAMVLADAMKRANSVDPKVFAPFLAKTEYKGVTANIAFTAKGELTTPAVTL 372

Query: 365 YVYKDGKKTPL 375
           Y +KDG +  L
Sbjct: 373 YTFKDGSRVAL 383


Lambda     K      H
   0.315    0.131    0.375 

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: 511
Number of extensions: 15
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 375
Length of database: 384
Length adjustment: 30
Effective length of query: 345
Effective length of database: 354
Effective search space:   122130
Effective search space used:   122130
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: 50 (23.9 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, or view the source code.

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